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1.  Effects of spermine NONOate and ATP on protein aggregation: light scattering evidences 
BMC Biophysics  2013;6:1.
Background and objective
Regulating protein function in the cell by small molecules, provide a rapid, reversible and tunable tool of metabolic control. However, due to its complexity the issue is poorly studied so far. The effects of small solutes on protein behavior can be studied by examining changes of protein secondary structure, in its hydrodynamic radius as well as its thermal aggregation. The study aim was to investigate effects of adenosine-5’-triphosphate (ATP), spermine NONOate (NO donor) as well as sodium/potassium ions on thermal aggregation of albumin and hemoglobin. To follow aggregation of the proteins, their diffusion coefficients were measured by quasi-elastic light scattering (QELS) at constant pH (7.4) in the presence of solutes over a temperature range from 25°C to 80°C.
Results and discussion
1) Spermine NONOate persistently decreased the hemoglobin aggregation temperature Tairrespectively of the Na+/K+ environment, 2) ATP alone had no effect on the protein’s thermal stability but it facilitated protein’s destabilization in the presence of spermine NONOate and 3) mutual effects of ATP and NO were strongly influenced by particular buffer ionic compositions.
Conclusion
The ATP effect on protein aggregation was ambiguous: ATP alone had no effect on the protein’s thermal stability but it facilitated protein’s destabilization in the presence of nitric oxide. The magnitude and direction of the observed effects strongly depended on concentrations of K+ and Na+ in the solution.
doi:10.1186/2046-1682-6-1
PMCID: PMC3561150  PMID: 23289636
2.  Systematic analysis of the ability of Nitric Oxide donors to dislodge biofilms formed by Salmonella enterica and Escherichia coli O157:H7 
AMB Express  2014;4:42.
Biofilms in the industrial environment could be problematic. Encased in extracellular polymeric substances, pathogens within biofilms are significantly more resistant to chlorine and other disinfectants. Recent studies suggest that compounds capable of manipulating nitric oxide-mediated signaling in bacteria could induce dispersal of sessile bacteria and provide a foundation for novel approaches to controlling biofilms formed by some microorganisms. In this work, we compared the ability of five nitric oxide donors (molsidomine, MAHMA NONOate, diethylamine NONOate, diethylamine NONOate diethylammonium salt, spermine NONOate) to dislodge biofilms formed by non-typhoidal Salmonella enterica and pathogenic E. coli on plastic and stainless steel surfaces at different temperatures. All five nitric oxide donors induced significant (35-80%) dispersal of biofilms, however, the degree of dispersal and the optimal dispersal conditions varied. MAHMA NONOate and molsidomine were strong dispersants of the Salmonella biofilms formed on polystyrene. Importantly, molsidomine induced dispersal of up to 50% of the pre-formed Salmonella biofilm at 4°C, suggesting that it could be effective even under refrigerated conditions. Biofilms formed by E. coli O157:H7 were also significantly dispersed. Nitric oxide donor molecules were highly active within 6 hours of application. To better understand mode of action of these compounds, we identified Salmonella genomic region recA-hydN, deletion of which led to an insensitivity to the nitric oxide donors.
doi:10.1186/s13568-014-0042-y
PMCID: PMC4070026  PMID: 24995149
Biofilm control; Bacterial signaling; Food-borne pathogens; Nitric oxide
3.  Cyclic GMP-independent relaxation of rat pulmonary artery by spermine NONOate, a diazeniumdiolate nitric oxide donor 
British Journal of Pharmacology  2000;131(4):673-682.
In rat pulmonary artery pre-contracted with phenylephrine, the mechanisms of relaxation to the nitric oxide (NO) donor, spermine NONOate, were investigated.Responses to spermine NONOate were only partially blocked by the soluble guanylate cyclase inhibitor, ODQ (1H-[1,2,4]Oxadiazolo-[4,3,-a]quinoxalin-1-one) at concentrations up to 30 μM. Ten μM ODQ gave maximal inhibition. Endothelium removal had no effect on the potency of spermine NONOate or its inhibition by ODQ.The protein kinase G inhibitor, Rp-8-Br-cGMPS (100 μM), caused minimal inhibition of spermine NONOate despite causing marked inhibition of glyceryl trinitrate and isosorbide dinitrate.Spermine NONOate (100 μM) caused a 35 fold increase in guanosine 3′5′ cyclic monophosphate (cyclic GMP) above basal levels in pulmonary artery rings. ODQ (3 μM) abolished this cyclic GMP production but did not inhibit corresponding relaxant responses. Similar results were seen with another NONOate (MAHMA NONOate; 10 μM).ODQ-resistant relaxation to spermine NONOate (i.e. relaxation seen in the presence of 10 μM ODQ) was inhibited by potassium (80 mM), charybdotoxin (300 nM), iberiotoxin (300 nM), apamin (100 nM), ouabain (1 mM) or thapsigargin (100 nM) but not by 4-aminopyridine (3 mM), glybenclamide (10 μM) or diltiazem (10 μM).Potassium, charybdotoxin, ouabain and thapsigargin also inhibited ODQ-resistant relaxation to FK409 ((±)-E-4-ethyl-2-[E-hydroxyimino]-5-nitro-3-hexenamide).We conclude that, on rat pulmonary artery, spermine NONOate can produce cyclic GMP-independent relaxation that involves, at least in part, activation of Na+/K+-ATPase, sarco-endoplasmic reticulum Ca2+-ATPase and calcium-activated potassium channels.
doi:10.1038/sj.bjp.0703613
PMCID: PMC1572374  PMID: 11030715
Calcium-activated potassium channels; cyclic GMP-independent relaxation; FK409; Na+/K+-ATPase; nitric oxide donors; rat pulmonary artery; sarco-endoplasmic reticulum Ca2+-ATPase; spermine NONOate
4.  Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection 
Physicochemical properties of molecules can be linked directly to evolutionary fates of a population in a quantitative and predictive manner.Reversible- and irreversible-folding pathways must be accounted for to accurately determine in vitro kinetic parameters (KM and kcat) at temperatures or conditions in which a significant fraction of free enzyme is unfolded.In vivo population dynamics can be reproduced using in vitro physicochemical measurements within a model that imposes an activity threshold above which there is no added fitness benefit.
In nature, evolution occurs through the continuous adaptation of a population to its environment. The success or failure of organisms during adaptation is based on changes in molecular structure that give rise to changes in fitness that dictate evolutionary fates within a population. Although the conceptual link between genotype, phenotype, and fitness is clear, the ability to relate these complex adaptive landscapes in a quantitative manner remains difficult (Kacser and Burns, 1981; Dykhuizen et al, 1987; Weinreich et al, 2006). Dean and Thornton (2007) coined the term ‘functional synthesis' to capture the synergy between evolutionary and molecular biology to address important questions such as the evolution of complexity. The ‘functional synthesis,' in its most fully realized form, is an integrated systems biology approach to evolutionary dynamics that links physicochemical properties of molecules to evolutionary fates in a quantitative and predictive manner.
Functional synthesis flourishes in an experimental framework that allows investigators to directly link population dynamics (fitness) to changes in molecular function that result from alterations at the nucleotide level. The ‘weak link' approach was developed to tightly couple adaptive changes within the genome to changes in fitness and provide a population-based approach that can be used to examine alterations in function and fitness at the level of atomic structure and function (Counago and Shamoo, 2005; Counago et al, 2006). A homologous recombination strategy was used to replace the chromosomal copy of the essential adenylate kinase gene (adk) of the thermophilic bacterium Geobacillus stearothermophilus with that of the mesophile Bacillus subtilis. Recombinant G. stearothermophilus cells that expressed only B. subtilis adenylate kinase (AKBSUB) were unable to grow at temperatures higher than 55°C because of heat inactivation of the mesophilic enzyme and consequent disruption of adenylate homeostasis (Counago and Shamoo, 2005). Continuously growing populations of bacteria were then subjected to selection at increasing temperatures (from 55 to 70°C) that favor changes in the one gene not adapted for thermostability, adk. During the course of selection, the population was sampled and intermediates of adaptation were observed as mutations to adk. The first mutant to reach fixation was a single mutation AKBSUB Q199R (the glutamine at position 199 replaced with arginine). AKBSUB Q199R was eventually replaced at 62–63°C by five double mutants that arose nearly simultaneously within the population and share AKBSUB Q199R as their progenitor (Figure 4C). Changes to AK activity and thermal stability that resulted from mutation had direct consequences for cellular fitness and, therefore, met our goal for an experimental system that allows us to develop and test models for quantitative molecular evolution. These enzyme activities and stabilities were examined to determine how the mutant populations traversed the adaptive landscape to increased fitness (Counago et al, 2006).
We found that reversible- and irreversible-folding pathways as well as a ‘physiological threshold' above which fitness changes are minimal are necessary to reproduce the in vivo evolutionary fates of the population. Protein-folding parameters must be accounted for to accurately determine in vitro kinetic parameters (KM and kcat) at temperatures in which a significant fraction of free enzyme is unfolded (Scheme I and Equation 1).
Scheme I
where
Thermostability was assayed using differential scanning calorimetry (DSC) (Figure 4A) and the fraction of unfolded protein (YU) was then extended to accurately predict the extent of stabilization, shift in Tm, in the presence of ligand. The kinetic parameters determined at specific temperatures were then used to construct a temperature-dependent formulation of Equation (1) to model in vitro activity at any given ATP concentration and any temperature (Figure 4B).
Here, we have modeled fitness as a function of in vitro enzyme activity, which is a product of both activity and stability, and the application of a threshold that provides an upper limit on fitness. We hypothesize that an activity threshold exists above which no added fitness benefit is attained (the ‘physiological threshold'). However, as activity falls below this threshold, AK becomes rate limiting and fitness is negatively affected. The experimentally observed rise and fall of mutant alleles is shown in Figure 4C, whereas those predicted from our in vitro model are shown as Figure 4D. This model can successfully reproduce frequencies of mutants in a polymorphic population, including the transient success of three minor mutants and order of disappearance from the population, given only in vitro data and allowing for the activity threshold to be fit to the observed outcomes (Figure 4D). An appealing aspect of our fitness function is that it permits an evaluation of specific and quantitative aspects of protein stability and activity relative to evolutionary fates.
In vivo, diversity within a population is generated by a variety of mechanisms that span single nucleotide changes to genome-wide rearrangements and horizontal gene transfer. However, changes are generated within an organism, it is the physicochemical characteristics of the resulting macromolecules and their resultant changes in the fitness of the organism that are the ‘grist for the mill' of natural selection. Recent work has shown that adaptability can be facilitated by the accumulation of near neutral or even modestly destabilizing mutations that provide more possibilities for success. Chaperones have an important function in buffering biological systems against these destabilizing mutations as well as mistakes in translation that lead to polymorphic populations and have been shown to increase rates of adaptation (Rutherford, 2003; Drummond and Wilke, 2008; Tokuriki and Tawfik, 2009a). Thus, adaptation through protein evolution is circumscribed by protein stability. As most mutational events will be destabilizing (Tokuriki and Tawfik, 2009b), higher mutation rates can lead to decreases in fitness eventually leading to extinction (Zeldovich et al, 2007; Chen and Shakhnovich, 2009). Although our system links the physicochemical properties of adaptive changes that increase stability, the principles apply equally to those changes that might decrease stability of the ensemble either through mutation or translational errors (Drummond and Wilke, 2008). Thus, regardless of how protein diversity is generated, evolutionary dynamics will likely be strongly coupled to stability and function.
Systems biology can offer a great deal of insight into evolution by quantitatively linking complex properties such as protein structure, folding, and function to the fitness of an organism. Although the link between diseases such as Alzheimer's and misfolding is well appreciated, directly showing the importance of protein folding to success in evolution has been more difficult. We show here that predicting success during adaptation can depend critically on enzyme kinetic and folding models. We used a ‘weak link' method to favor mutations to an essential, but maladapted, adenylate kinase gene within a microbial population that resulted in the identification of five mutants that arose nearly simultaneously and competed for success. Physicochemical characterization of these mutants showed that, although steady-state enzyme activity is important, success within the population is critically dependent on resistance to denaturation and aggregation. A fitness function based on in vitro measurements of enzyme activity, reversible and irreversible unfolding, and the physiological context reproduces in vivo evolutionary fates in the population linking organismal adaptation to its physical basis.
doi:10.1038/msb.2010.43
PMCID: PMC2925523  PMID: 20631681
adenylate kinase; enzyme kinetics; experimental evolution; fitness functions; protein folding
5.  Nitric oxide increases cyclic GMP levels, AMP-activated protein kinase (AMPK)α1-specific activity and glucose transport in human skeletal muscle 
Diabetologia  2010;53(6):1142-1150.
Aims/hypothesis
We investigated the direct effect of a nitric oxide donor (spermine NONOate) on glucose transport in isolated human skeletal muscle and L6 skeletal muscle cells. We hypothesised that pharmacological treatment of human skeletal muscle with N-(2-aminoethyl)-N-(2-hydroxy-2-nitrosohydrazino)-1,2-ethylenediamine (spermine NONOate) would increase intracellular cyclic GMP (cGMP) levels and promote glucose transport.
Methods
Skeletal muscle strips were prepared from vastus lateralis muscle biopsies obtained from seven healthy men. Muscle strips were incubated in the absence or presence of 5 mmol/l spermine NONOate or 120 nmol/l insulin. The L6 muscle cells were treated with spermine NONOate (20 µmol/l) and incubated in the absence or presence of insulin (120 nmol/l). The direct effect of spermine NONOate and insulin on glucose transport, cGMP levels and signal transduction was determined.
Results
In human skeletal muscle, spermine NONOate increased glucose transport 2.4-fold (p < 0.05), concomitant with increased cGMP levels (80-fold, p < 0.001). Phosphorylation of components of the canonical insulin signalling cascade was unaltered by spermine NONOate exposure, implicating an insulin-independent signalling mechanism. Consistent with this, spermine NONOate increased AMP-activated protein kinase (AMPK)-α1-associated activity (1.7-fold, p < 0.05). In L6 muscle cells, spermine NONOate increased glucose uptake (p < 0.01) and glycogen synthesis (p < 0.001), an effect that was in addition to that of insulin. Spermine NONOate also elicited a concomitant increase in AMPK and acetyl-CoA carboxylase phosphorylation. In the presence of the guanylate cyclase inhibitor LY-83583 (10 µmol/l), spermine NONOate had no effect on glycogen synthesis and AMPK-α1 phosphorylation.
Conclusions/interpretation
Pharmacological treatment of skeletal muscle with spermine NONOate increases glucose transport via insulin-independent signalling pathways involving increased intracellular cGMP levels and AMPK-α1-associated activity.
doi:10.1007/s00125-010-1716-x
PMCID: PMC2860569  PMID: 20349036
Contraction; Exercise; GLUT4; Spermine NONOate
6.  Buffer-dependent fragmentation of a humanized full-length monoclonal antibody 
Journal of pharmaceutical sciences  2010;99(7):2962-2974.
During storage stability studies of a monoclonal antibody (mAb) it was determined that the primary route of degradation involved fragmentation into lower molecular weight species. The fragmentation was characterized with size-exclusion high performance liquid chromatography (SE-HPLC), SDS-PAGE and matrix assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry. Fragmentation proceeded via hydrolysis, likely catalyzed by trace metal ions, of a peptide bond in the hinge region of the mAb’s heavy chain, which produced two prominent low molecular weight species during storage: a single, free Fab fragment and a Fab+Fc fragment. The fragmentation is observed in phosphate-buffered solutions at two ionic strengths but not in histidine-buffered solutions at identical ionic strengths. Chaotrope-induced and thermally-induced unfolding studies of the mAb indicated differences in the unfolding pathways between the two buffer solutions. This folding intermediate observed during chaotrope-induced unfolding was further characterized by intrinsic fluorescence quenching, which suggested that a small portion of the molecule is resistant to chaotrope-induced unfolding in histidine buffer systems. The thermally-induced unfolding indicates a reduction in cooperativity of the unfolding process in the presence of histidine relative to phosphate. A relationship between the histidine-induced effects on unfolding pathway and the relative resistance to fragmentation is suggested.
doi:10.1002/jps.22056
PMCID: PMC3938388  PMID: 20091831
7.  AMPylation matches BiP activity to client protein load in the endoplasmic reticulum 
eLife  null;4:e12621.
The endoplasmic reticulum (ER)-localized Hsp70 chaperone BiP affects protein folding homeostasis and the response to ER stress. Reversible inactivating covalent modification of BiP is believed to contribute to the balance between chaperones and unfolded ER proteins, but the nature of this modification has so far been hinted at indirectly. We report that deletion of FICD, a gene encoding an ER-localized AMPylating enzyme, abolished detectable modification of endogenous BiP enhancing ER buffering of unfolded protein stress in mammalian cells, whilst deregulated FICD activity had the opposite effect. In vitro, FICD AMPylated BiP to completion on a single residue, Thr518. AMPylation increased, in a strictly FICD-dependent manner, as the flux of proteins entering the ER was attenuated in vivo. In vitro, Thr518 AMPylation enhanced peptide dissociation from BiP 6-fold and abolished stimulation of ATP hydrolysis by J-domain cofactor. These findings expose the molecular basis for covalent inactivation of BiP.
DOI: http://dx.doi.org/10.7554/eLife.12621.001
eLife digest
Newly made proteins are unstructured chains of amino acids that must fold into particular shapes to work effectively. Proteins that are destined to be exported from the cell undergo folding in a compartment of the cell called the endoplasmic reticulum. This folding is assisted by chaperones (which are themselves also proteins).
Cells adjust the number of chaperones so that there are enough to cope with the burden of unfolded proteins. However, in the endoplasmic reticulum, the known mechanisms that regulate the production of chaperones are too slow to track the rapid fluctuations in the production of unfolded proteins. This suggests that other means exist to balance active chaperones and unfolded proteins that go beyond merely controlling chaperone or unfolded protein abundance.
An important chaperone protein of the endoplasmic reticulum, called BiP, is chemically modified when the production of unfolded proteins declines, and loses the modification when more unfolded proteins are produced. This suggests that the modification might adjust BiP’s activity so that it can handle the unfolded proteins that are present. However, previous studies have failed to agree about the nature of the chemical modification and how it affects how BiP works.
Preissler, Rato et al. compared the activity of BiP in normal mammalian cells and in cells engineered to lack an enzyme called FICD. This enzyme attaches a molecule of adenosine mono-phosphate (AMP) to proteins in a process known as AMPylation. The experiments revealed that AMPylation is the modification of BiP that tracks how many unfolded proteins are in the cell. Further studies showed that AMP attaches to a single amino acid of BiP, number 518, a threonine. Reconstructing the AMPylation of threonine 518 in a test tube caused the modified BiP to lose its ability to engage with unfolded proteins.
Overall, Preissler, Rato et al.’s results indicate that cells inactivate BiP by AMPylating threonine 518 as the number of unfolded proteins decreases, and remove the modification to re-activate BiP in response to mounting levels of unfolded proteins. Further studies are now needed to determine how AMPylation inactivates BiP and to understand how the FICD enzyme is regulated so that it performs AMPylation at the right time. It also remains to be explored how important the regulation of BiP activity by AMPylation is for living cells.
DOI: http://dx.doi.org/10.7554/eLife.12621.002
doi:10.7554/eLife.12621
PMCID: PMC4739761  PMID: 26673894
BiP/GRP78; AMPylation; FICD/HYPE; Hsp70; chaperones; endoplasmic reticulum; None
8.  Thermal, Chemical and pH Induced Unfolding of Turmeric Root Lectin: Modes of Denaturation 
PLoS ONE  2014;9(8):e103579.
Curcuma longa rhizome lectin, of non-seed origin having antifungal, antibacterial and α-glucosidase inhibitory activities, forms a homodimer with high thermal stability as well as acid tolerance. Size exclusion chromatography and dynamic light scattering show it to be a dimer at pH 7, but it converts to a monomer near pH 2. Circular dichroism spectra and fluorescence emission maxima are virtually indistinguishable from pH 7 to 2, indicating secondary and tertiary structures remain the same in dimer and monomer within experimental error. The tryptophan environment as probed by acrylamide quenching data yielded very similar data at pH 2 and pH 7, implying very similar folding for monomer and dimer. Differential scanning calorimetry shows a transition at 350.3 K for dimer and at 327.0 K for monomer. Thermal unfolding and chemical unfolding induced by guanidinium chloride for dimer are both reversible and can be described by two-state models. The temperatures and the denaturant concentrations at which one-half of the protein molecules are unfolded, are protein concentration-dependent for dimer but protein concentration-independent for monomer. The free energy of unfolding at 298 K was found to be 5.23 Kcal mol−1 and 14.90 Kcal mol−1 for the monomer and dimer respectively. The value of change in excess heat capacity upon protein denaturation (ΔCp) is 3.42 Kcal mol−1 K−1 for dimer. The small ΔCp for unfolding of CLA reflects a buried hydrophobic core in the folded dimeric protein. These unfolding experiments, temperature dependent circular dichroism and dynamic light scattering for the dimer at pH 7 indicate its higher stability than for the monomer at pH 2. This difference in stability of dimeric and monomeric forms highlights the contribution of inter-subunit interactions in the former.
doi:10.1371/journal.pone.0103579
PMCID: PMC4139268  PMID: 25140525
9.  Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease 
PLoS Computational Biology  2010;6(2):e1000689.
Kinetically stable proteins, those whose stability is derived from their slow unfolding kinetics and not thermodynamics, are examples of evolution's best attempts at suppressing unfolding. Especially in highly proteolytic environments, both partially and fully unfolded proteins face potential inactivation through degradation and/or aggregation, hence, slowing unfolding can greatly extend a protein's functional lifetime. The prokaryotic serine protease α-lytic protease (αLP) has done just that, as its unfolding is both very slow (t1/2 ∼1 year) and so cooperative that partial unfolding is negligible, providing a functional advantage over its thermodynamically stable homologs, such as trypsin. Previous studies have identified regions of the domain interface as critical to αLP unfolding, though a complete description of the unfolding pathway is missing. In order to identify the αLP unfolding pathway and the mechanism for its extreme cooperativity, we performed high temperature molecular dynamics unfolding simulations of both αLP and trypsin. The simulated αLP unfolding pathway produces a robust transition state ensemble consistent with prior biochemical experiments and clearly shows that unfolding proceeds through a preferential disruption of the domain interface. Through a novel method of calculating unfolding cooperativity, we show that αLP unfolds extremely cooperatively while trypsin unfolds gradually. Finally, by examining the behavior of both domain interfaces, we propose a model for the differential unfolding cooperativity of αLP and trypsin involving three key regions that differ between the kinetically stable and thermodynamically stable classes of serine proteases.
Author Summary
Proteins, synthesized as linear polymers of amino acids, fold up into compact native states, burying their hydrophobic amino acids into their interiors. Protein folding minimizes the non-specific interactions that unfolded protein chains can make, which include aggregation with other proteins and degradation by proteases. Unfortunately, even in the native state, proteins can partially unfold, opening up regions of their structure and making these adverse events possible. Some proteins, particularly those in harsh environments full of proteases, have evolved to virtually eliminate partial unfolding, significantly reducing their rate of degradation. This elimination of partial unfolding is termed “cooperative,” because unfolding is an all-or-none process. One class of proteins has diverged into two families, one bacterial and highly cooperative and the other animal and non-cooperative. We have used detailed simulations of unfolding for members of each family, α-lytic protease (bacterial) and trypsin (animal) to understand the unfolding pathways of each and the mechanism for the differential unfolding cooperativity. Our results explain prior biochemical experiments, reproduce the large difference in unfolding cooperativity between the families, and point to the interface between α-lytic protease's two domains as essential to establishing unfolding cooperativity. As seen in an unrelated protein family, generation of a cooperative domain interface may be a common evolutionary response for ensuring the highest protein stability.
doi:10.1371/journal.pcbi.1000689
PMCID: PMC2829044  PMID: 20195497
10.  Biophysical Analysis of Progressive C-Terminal Truncations of Human Apolipoprotein E4: Insights into Secondary Structure and Unfolding Properties 
Biochemistry  2008;47(35):9071-9080.
Apolipoprotein E4 (apoE4) is a risk factor for Alzheimer’s disease and has been associated with a variety of neuropathological processes. ApoE4 C-terminally truncated forms have been found in brains of Alzheimer’s disease patients. Structural rearrangements in apoE4 are known to be key to its physiological functions. To understand the effect of C-terminal truncations on apoE4 lipid-free structure, we produced a series of recombinant apoE4 forms with progressive C-terminal deletions between residues 166 and 299. Circular dichroism measurements show a dramatic loss in helicity upon removal of the last 40 C-terminal residues, whereas further truncations of residues 203–259 lead to recovery of helical content. Further deletion of residues 186–202 leads to a small increase in helical content. Thermal denaturation indicated that removal of residues 260–299 leads to an increase in melting temperature but truncations down to residue 186 did not further affect the melting temperature. The progressive C-terminal truncations, however, gradually increased the cooperativity of thermal unfolding. Chemical denaturation of the apoE4 forms revealed a two-step process with a clear intermediate stage that is progressively lost as the C-terminus is truncated down to residue 230. Hydrophobic fluorescent probe binding suggested that regions 260–299 and 186–202 contain hydrophobic sites, the former being solvent accessible in the wild-type molecule and the latter being accessible only upon truncation. Taken together, our results show an important but complex role of apoE4 C-terminal segments in secondary structure stability and unfolding and suggest that interactions mediated by the C-terminal segments are important for the structural integrity and conformational changes of apoE4.
doi:10.1021/bi800469r
PMCID: PMC2692411  PMID: 18690708
11.  Hydroxyurea stimulates the release of ATP from rabbit erythrocytes through an increase in calcium and nitric oxide production 
European journal of pharmacology  2010;645(0):32-38.
Hydroxyurea, a proven therapy for sickle cell disease, is known to improve blood flow and reduce vaso-occlusive crises, although its exact mechanism of action is not clear. The objective of this study was to determine if hydroxyurea results in an increase of ATP release from the red blood cell (RBC) via the drug's ability to stimulate nitric oxide (NO) production in these cells. A system enabling the flow of RBCs through microbore tubing was used to investigate ATP release from the RBC. Incubation of rabbit RBCs (7% hct) with 50 μM hydroxyurea resulted in a significant increase in the release of ATP from these cells. This level of ATP release was not detected in the absence of flow. Studies also showed that increments in hydroxyurea and NO (from spermineNONOate) resulted in an initial increase in ATP release, followed by a decrease in this release at higher concentrations of hydroxyurea and the NO donor. Incubation with L-NAME abolished the effect of the hydroxyurea, suggesting that NO production by the RBC was involved. Indeed, in the presence of 50 μM hydroxyurea, the amount of total Ca2+ measured (by atomic absorption spectroscopy) in a 7% solution of RBCs increased from 363 ± 47 ng/ml and 530 ± 52 ng/ml. Finally, EPR studies suggest that an increase in nitrosylated Hb in the RBC is only measured for those studies involving hydroxyurea and a Ca2+-containing buffer.
doi:10.1016/j.ejphar.2010.07.012
PMCID: PMC4051288  PMID: 20655902
nitric oxide; hydroxyurea; ATP; eNOS; red cells; sickle cell
12.  ProteoPlex - stability optimization of macromolecular complexes by sparse-matrix screening of chemical space 
Nature methods  2015;12(9):859-865.
Molecular machines or macromolecular complexes are supramolecular assemblies of biomolecules that ensure cellular homeostasis. Structure determination of those complexes in a purified state is often a tedious undertaking due to the compositional complexity and the related relative structural instability. To improve the stability of macromolecular complexes in vitro, we present here a generic method that optimizes the stability, homogeneity and solubility of macromolecular complexes by sparse-matrix screening of their thermal unfolding behaviour in the presence of various buffers and small molecules. The method includes the automated analysis of thermal unfolding curves based on a newly developed biophysical unfolding model for complexes. We found that under stabilizing conditions even large multi-component complexes reveal an almost ideal two-state unfolding behaviour. We envisage an improved biochemical understanding of purified macromolecules as well as a substantial boost in successful macromolecular complex structure determination by both X-ray crystallography and Cryo EM.
doi:10.1038/nmeth.3493
PMCID: PMC5136620  PMID: 26237227
13.  Measurement of the Effect of Monovalent Cations on RNA Hairpin Stability 
Journal of the American Chemical Society  2007;129(48):14966-14973.
Using optical tweezers, we have measured the effect of monovalent cation concentration and species on the folding free energy of five large (49-124 nt) RNA hairpins, including HIV-1 TAR and molecules approximating A·U and G·C homopolymers. RNA secondary structure thermodynamics are accurately described by a model consisting of nearest-neighbor interactions and additive loop and bulge terms. Melting of small (<15 bp) duplexes and hairpins in 1M NaCl has been used to determine the parameters of this model, which is now used extensively to predict structure and folding dynamics. Few systematic measurements have been made in other ionic conditions or for larger structures. By applying mechanical force, we measured the work required to fold and unfold single hairpins at room temperature over a range of cation concentrations from 50 to 1000 mM. Free energies were then determined using the Crooks Fluctuation Theorem. We observed the following: 1. In most cases, the nearest neighbor model accurately predicted the free energy of folding at 1M NaCl. 2. Free energy was proportional to the logarithm of salt concentration. 3. Substituting potassium ions for sodium slightly decreased hairpin stability. The TAR hairpin also misfolded nearly twice as often in KCl, indicating a differential kinetic response. 4. Monovalent cation concentration affects RNA stability in a sequence-dependent manner. G·C helices were unaffected by changing salt concentration, A·U helices were modestly affected, and the hairpin loop was very sensitive. Surprisingly, the UCU bulge of TAR was found to be equally stable in all conditions tested. We also report a new estimate for the elastic parameters of single-stranded RNA.
doi:10.1021/ja074809o
PMCID: PMC2528546  PMID: 17997555
14.  A Biochemical-Biophysical Study of Hemoglobins from Woolly Mammoth, Asian Elephant, and Humans† 
Biochemistry  2011;50(34):7350-7360.
This study is aimed at investigating the molecular basis of environmental adaptation of woolly mammoth hemoglobin (Hb) to the harsh thermal conditions of the Pleistocene Ice-ages. To this end, we have carried out a comparative biochemical-biophysical characterization of the structural and functional properties of recombinant hemoglobins (rHb) from woolly mammoth (rHb WM) and Asian elephant (rHb AE) in relation to human hemoglobins Hb A and Hb A2 (a minor component of human Hb). We have obtained oxygen equilibrium curves and calculated O2 affinities, Bohr effects, and the apparent heat of oxygenation (ΔH) in the presence and absence of allosteric effectors [inorganic phosphate and inositol hexaphosphate (IHP)]. Here, we show that the four Hbs exhibit distinct structural properties and respond differently to allosteric effectors. In addition, the apparent heat of oxygenation (ΔH) for rHb WM is less negative than that of rHb AE, especially in phosphate buffer and the presence of IHP, suggesting that the oxygen affinity of mammoth blood was also less sensitive to temperature change. Finally, 1H-NMR spectroscopy data indicates that both α1(β/δ)1 and α1(β/δ)2 interfaces in rHb WM and rHb AE are perturbed, whereas only the α1δ1 interface in Hb A2 is perturbed compared to that in Hb A. The distinct structural and functional features of rHb WM presumably facilitated woolly mammoth survival in the Arctic environment.
doi:10.1021/bi200777j
PMCID: PMC3160526  PMID: 21806075
15.  Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin 
PLoS Computational Biology  2013;9(1):e1002864.
Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all aspects of the protein's mechanical behavior, including the order of repeat unfolding, the diversity of unfolding pathways accessed, the nature of partially unfolded intermediates, the forces required and the work transferred to the system to unfold the whole protein and its parts. Stepwise unfolding thus provides the means to buffer repeat proteins and their binding partners from mechanical stress in the cell. Our results illustrate how ligand binding can control the mechanical response of proteins. The data also point to a cellular mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress.
Author Summary
Here we use molecular dynamics simulation to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with binding partner S6-C. Tandem repeat proteins like Gankyrin comprise tandem arrays of small structural motifs that pack linearly to produce elongated architectures. They are elastic, mechanically weak molecules and they unfold and refold repeat by repeat under force. We show that S6-C binding greatly increases the resistance of Gankyrin to mechanical stress. The enhanced mechanical stability is specific to those ankyrin repeats in contact with S6-C, and the localized nature of the effect results in fundamental changes in the way the protein responds to force. Thus, the forced unfolding of isolated Gankryin involves a diverse set of pathways with a preference for a C- to N-terminus unfolding mechanism whereas this diversity is reduced upon complex formation with the central repeats, which are those most tightly bound to the ligand, tending to unfold last. Our study shows how stepwise unfolding can buffer repeat proteins and their binding partners from mechanical stress in the cell. It also points to a mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress.
doi:10.1371/journal.pcbi.1002864
PMCID: PMC3547791  PMID: 23341763
16.  Inhibition of rat platelet aggregation by the diazeniumdiolate nitric oxide donor MAHMA NONOate 
British Journal of Pharmacology  2002;137(7):1071-1081.
Inhibition of rat platelet aggregation by the nitric oxide (NO) donor MAHMA NONOate (Z-1-{N-methyl-N-[6-(N-methylammoniohexyl)amino]}diazen-1-ium-1,2-diolate) was investigated. The aims were to compare its anti-aggregatory effect with vasorelaxation, to determine the effects of the soluble guanylate cyclase inhibitor, ODQ (1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one), and to investigate the possible role of activation of sarco-endoplasmic reticulum calcium-ATPase (SERCA), independent of soluble guanylate cyclase, using thapsigargin.MAHMA NONOate concentration-dependently inhibited sub-maximal aggregation responses to collagen (2–10 μg ml−1) and adenosine diphosphate (ADP; 2 μM) in platelet rich plasma. It was (i) more effective at inhibiting aggregation induced by collagen than by ADP, and (ii) less potent at inhibiting platelet aggregation than relaxing rat pulmonary artery.ODQ (10 μM) caused only a small shift (approximately half a log unit) in the concentration-response curve to MAHMA NONOate irrespective of the aggregating agent.The NO-independent activator of soluble guanylate cyclase, YC-1 (3-(5′-hydroxymethyl-2′-furyl)-1-benzyl indazole; 1–100 μM), did not inhibit aggregation. The cGMP analogue, 8-pCPT-cGMP (8-(4-chlorophenylthio)guanosine 3′5′ cyclic monophosphate; 0.1–1 mM), caused minimal inhibition.On collagen-aggregated platelets responses to MAHMA NONOate (ODQ 10 μM present) were abolished by thapsigargin (200 nM). On ADP-aggregated platelets thapsigargin caused partial inhibition.Results with S-nitrosoglutathione (GSNO) resembled those with MAHMA NONOate. Glyceryl trinitrate and sodium nitroprusside were poor inhibitors of aggregation.Thus inhibition of rat platelet aggregation by MAHMA NONOate (like GSNO) is largely ODQ-resistant and, by implication, independent of soluble guanylate cyclase. A likely mechanism of inhibition is activation of SERCA.
doi:10.1038/sj.bjp.0704971
PMCID: PMC1573589  PMID: 12429580
MAHMA NONOate; nitric oxide donor drugs; ODQ; ODQ-resistant responses; rat platelet aggregation; sarco-endoplasmic reticulum calcium-ATPase; soluble guanylate cyclase inhibitor
17.  Effect of nitric oxide donors S-nitroso-N-acetyl-DL-penicillamine, Spermine and PAPA NONOate on intracellular pH in cardiomyocytes 
Summary
Previous studies have suggested that exogenous nitric oxide (NO) and NO-dependent signalling pathways modulate intracellular pH (pHi) in different cell types, but the role of NO in pHi regulation in the heart is poorly understood. Therefore, in this study we investigated the effect of NO donors S-nitroso-N-acetyl-DL-penicillamine, Spermine and PAPA NONOate on pHi in isolated rat ventricular myocytes.The cells were isolated from the hearts of adult Wistar rats, and pHi was monitored using a pH-sensitive fluorescent indicator 5-(and-6)-carboxy SNARF-1 with a confocal microscope. To test the effect of NO donors on sodium-hydrogen exchanger, basal pHi in Na+-free buffer and pHi recovery from intracellular acidosis after an ammonium chloride prepulse were monitored. The role of carbonic anhydrase was tested using acetazolamide. Cl−-OH− and Cl−-HCO3− exchangers were inhibited with 4,4 diisothiocyanatostilbene 2,2' disulfonic acid.All three NO donors acutely decreased pHi. This effect lasted until NO donor was removed. In a Na+-free buffer decrease in basal pHi was increased, while inhibition of carbonic anhydrase and Cl−-OH− and Cl−-HCO3− exchangers did not change the effect of NO donors on pHi. After an ammonium preload, pHi recovery was accelerated in the presence of NO donors.In conclusion, exogenous NO decreased the basal pHi leading to increased activity of sodium-hydrogen exchanger. Carbonic anhydrase and chloride-dependent sarcolemmal HCO3− and OH− transporters are not involved in the NO-induced pHi decrease in isolated rat ventricular myocytes.
doi:10.1111/j.1440-1681.2012.05734.x
PMCID: PMC3430815  PMID: 22703333
Nitric oxide; intracellular pH; cardiac myocytes; sodium hydrogen exchanger; carbonic anhydrase
18.  Spermine modulation of specific [3H]-gabapentin binding to the detergent-solubilized porcine cerebral cortex α2δ calcium channel subunit 
British Journal of Pharmacology  1997;120(5):833-840.
Recent studies have identified the [3H]-gabapentin-binding protein, purified from porcine cerebral cortical membranes, as the α2δ subunit of voltage-sensitive calcium channels (Gee et al., 1996). The present study investigates the influence of the polyamine spermine on specific [3H]-gabapentin binding to detergent-solubilized porcine cerebral cortical membranes.Spermine, spermidine, 1,10 diaminodecane, Mg2+ and Zn2+, all divalent cations, displaced [3H]-gabapentin binding to detergent-solubilized membranes in a concentration-dependent manner with a maximal inhibition of 65–75%. Radioligand binding studies showed that spermine did not directly interact with the [3H]-gabapentin-binding site. Spermine inhibited [3H]-gabapentin binding by interacting with a polyamine-sensitive allosteric site on the membrane protein. The steep concentration-dependence of spermine inhibition of [3H]-gabapentin binding may suggest multi-site co-operativity.Prolonged dialysis of cerebral cortical membranes and Tween 20-solubilized membranes resulted in a >2.0 fold increase in [3H]-gabapentin binding. The increase in binding was due to the removal of a heat stable, low molecular weight (<12,000Da) endogenous molecule which influences [3H]-gabapentin binding competitively.Dialysis of detergent-solubilized cerebral cortical membranes also resulted in a decrease in the maximum inhibition of [3H]-gabapentin binding by spermine. Since the rates of the increase in [3H]-gabapentin binding and the loss of the ability of spermine to inhibit [3H]-gabapentin binding on dialysis were different it was inferred that a second endogenous ligand was removed during dialysis.During initial steps of purification of the [3H]-gabapentin-binding protein there was a decrease in the maximum inhibition of [3H]-gabapentin binding by spermine. The loss of the second endogenous molecule during initial purification would reasonably explain the reduction in inhibition of binding by spermine. However, spermine stimulation of [3H]-gabapentin binding to material that eluted from the gel-filtration column later in the purification scheme does not appear to be due to removal of a dialysable endogenous factor or to the dissociation of other calcium channel subunit(s).Adding back dialysate, before or after boiling, to detergent solubilized membranes resulted in a dose-dependent restoration of the inhibition of [3H]-gabapentin binding and of the maximal inhibition [3H]-gabapentin binding by spermine. This result is consistent with the re-addition of two endogenous heat stable ligands.The finding that [3H]-gabapentin binding to the pure α2δ subunit was stimulated by spermine indicates that the α2δ subunit of voltage-sensitive calcium channels bears a modulatory spermine site. Such a spermine site has not been identified before. Spermine stimulation of [3H]-gabapentin binding to the purified protein was reversed to inhibition after adding back dialysate. Thus the inhibitory spermine effect in membranes is also probably due to one or more modulatory sites on the α2δ subunit.
doi:10.1038/sj.bjp.0700988
PMCID: PMC1564548  PMID: 9138689
Gabapentin; neurontin; calcium channels; α2δ subunit; anticonvulsant; polyamines; spermine; spermine modulation; N-methyl-D-aspartate (NMDA); endogenous ligand
19.  Thermodynamics of membrane insertion and refolding of the diphtheria toxin T-domain 
The Journal of membrane biology  2014;248(3):383-394.
The diphtheria toxin translocation (T) domain inserts into the endosomal membrane in response to the endosomal acidification and enables the delivery of the catalytic domain into the cell. The insertion pathway consists of a series of conformational changes that occur in solution and in the membrane and leads to the conversion of a water-soluble state into a transmembrane state. In this work, we utilize various biophysical techniques to characterize the insertion pathway from the thermodynamic perspective. Thermal and chemical unfolding measured by differential scanning calorimetry, circular dichroism and tryptophan fluorescence reveal that the free energy of unfolding of the T-domain at neutral and mildly acidic pH differ by 3–5 kcal/mol, depending on the experimental conditions. Fluorescence correlation spectroscopy measurements show that the free energy change from the membrane-competent state to the interfacial state is approximately −8 kcal/mol and is pH-independent, while that from the membrane-competent state to the transmembrane state ranges between −9.5 to −12 kcal/mol, depending on the membrane lipid composition and pH. Finally, the thermodynamics of transmembrane insertion of individual helices was tested using an in vitro assay that measures the translocon-assisted integration of test sequences into the microsomal membrane. These experiments suggest that even the most hydrophobic helix TH8 has only a small favorable free energy of insertion. The free energy for the insertion of the consensus insertion unit TH8-TH9 is slightly more favorable, yet less favorable than that measured for the entire protein, suggesting a cooperative effect for the membrane insertion of the helices of the T-domain.
doi:10.1007/s00232-014-9734-0
PMCID: PMC4385515  PMID: 25281329
20.  Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure 
Nucleic Acids Research  2001;29(24):5121-5128.
The effects of ions (i.e. Na+, Mg2+ and polyamines including spermidine and spermine) on the stability of various DNA oligonucleotides in solution were studied. These synthetic DNA molecules contained sequences that mimic various cellular DNA structures, such as duplexes, bulged loops, hairpins and/or mismatched base pairs. Melting temperature curves obtained from the ultraviolet spectroscopic experiments indicated that the effectiveness of the stabilization of cations on the duplex formation follows the order of spermine > spermidine > Mg2+ > Na+ > Tris–HCl buffer alone at pH 7.3. Circular dichroism spectra showed that salts and polyamines did not change the secondary structures of those DNA molecules under study. Surface plasmon resonance (SPR) observations suggested that the rates of duplex formation are independent of the kind of cations used or the structure of the duplexes. However, the rate constants of DNA duplex dissociation decrease in the same order when those cations are involved. The enhancement of the duplex stability by polyamines, especially spermine, can compensate for the instability caused by abnormal structures (e.g. bulged loops, hairpins or mismatches). The effects can be so great as to make the abnormal DNAs as stable as the perfect duplex, both kinetically and thermodynamically. Our results may suggest that the interconversion of various DNA structures can be accomplished readily in the presence of polyamine. This may be relevant in understanding the role of DNA polymorphism in cells.
PMCID: PMC97540  PMID: 11812845
21.  FTIR Studies of Collagen Model Peptides: Complementary Experimental and Simulation Approaches to Conformation and Unfolding 
X-ray crystallography of collagen model peptides has provided high resolution structures of the basic triple-helical conformation and its water-mediated hydration network. Vibrational spectroscopy provides a useful bridge for transferring the structural information from x-ray diffraction to collagen in its native environment. The vibrational mode most useful for this purpose is the Amide I mode (mostly peptide bond C=O stretch) near 1650 cm−1. The current study refines and extends the range of utility of a novel simulation method that accurately predicts the IR Amide I spectral contour from the three dimensional structure of a protein or peptide. The approach is demonstrated through accurate simulation of the experimental Amide I contour in solution for both a standard triple-helix, (Pro-Pro-Gly)10, and a second peptide with a Gly → Ala substitution in the middle of the chain that models the effect of a mutation in the native collagen sequence. Monitoring the major Amide I peak as a function of temperature gives sharp thermal transitions for both peptides, similar to those obtained by circular dichroism spectroscopy, and the FTIR spectra of the unfolded states were compared with polyproline II.
The simulation studies were extended to model early stages of thermal denaturation of (Pro-Pro-Gly)10. Dihedral angle changes suggested by molecular dynamics simulations were made in a stepwise fashion to generate peptide unwinding from each end, which emulates the effect of increasing temperature. Simulated bands from these new structures were then compared to the experimental bands obtained as temperature was increased. The similarity between the simulated and experimental IR spectra lends credence to the simulation method, and paves the way for a variety of applications.
doi:10.1021/ja071154i
PMCID: PMC2570338  PMID: 17550251
22.  Effects of urea on the microstructure and phase behavior of aqueous solutions of polyoxyethylene surfactants 
Membrane proteins are made soluble in aqueous buffers by the addition of various surfactants (detergents) to form so-called protein-detergent complexes (PDCs). Properties of membrane proteins are commonly assessed by unfolding the protein in the presence of surfactant in a buffer solution by adding urea. The stability of the protein under these conditions is then monitored by biophysical methods such as fluorescence or circular dichroism spectroscopy. Often overlooked in these experiments is the effect of urea on the phase behavior and micellar microstructure of the different surfactants used to form the PDCs. Here the effect of urea on five polyoxyethylene surfactants – n-octylytetraoxyethylene (C8E4), n-octylpentaoxyethylene (C8E5), n-decylhexaoxyethylene (C10E6), n-dodecylhexaoxyethylene (C12E6) and n-dodecyloctaoxylethylene (C12E8) – is explored. The presence of urea increases the critical micelle concentration (CMC) of all surfactants studied, indicating that the concentration of both the surfactant and urea should be considered in membrane protein folding studies. The cloud point temperature of all surfactants studied also increases with increasing urea concentration. Small-angle neutron scattering shows a urea-induced transition from an elongated to a globular shape for micelles of C8E4 and C12E6. In contrast, C8E5 and C12E8 form more globular micelles at room temperature and the micelles remain globular as the urea concentration is increased. The effects of increasing urea concentration on micelle structure are analogous to those of decreasing the temperature. The large changes in micelle structure observed here could also affect membrane protein unfolding studies by changing the structure of the PDC.
doi:10.1021/ie101011v
PMCID: PMC3045059  PMID: 21359094
23.  Hemoglobin stability: observations on the denaturation of normal and abnormal hemoglobins by oxidant dyes, heat, and alkali 
Journal of Clinical Investigation  1970;49(12):2369-2376.
Several unstable mutant hemoglobins have alterations which affect areas of the molecule involved in the attachment of heme to globin. Loss of heme from globin has been demonstrated during the denaturation of some of these unstable mutants. The importance of heme ligands for the stability of hemoglobin was illustrated in the present experiments on the denaturation of several hemoglobins and hemoglobin derivatives by heat, oxidative dyes, and alkali. Heating of normal hemolysates diluted to 4 g of hemoglobin per 100 ml at 50°C for 20 hr in 0.05 M sodium phosphate, pH 7.4, caused precipitation of 23-54% of the hemoglobin. Dialysis against water or dilution of the sample decreased denaturation to 12-20%. Precipitation was decreased to less than 3.5% by the presence of 0.015 M potassium cyanide. Increasing the ionic strength of the medium increased precipitation. Cyanide prevented the formation of inclusion bodies when red cells containing unstable hemoglobin Philly, β35 tyr → phe, were incubated with the redox dye new methylene blue. Conversion to methemoglobin increased the rate of alkali denaturation of hemoglobin but the presence of potassium cyanide returned the denaturation rate to that of ferrohemoglobin. The ability of cyanide to decrease heat precipitation of hemoglobin may depend on a dimeric or tetrameric state of the hemoglobin molecule. Purified β-chains, which exist as tetramers, were stabilized but purified monomeric α-chains were not rendered more heat resistant by the ligand. Stabilization of hemoglobin by cyanide required binding of the ligand to only one heme of an αβ-dimer. Hemoglobin Gun Hill, an unstable molecule with heme groups present only on the α-chains was quite heat stable in the presence of cyanide. The binding of cyanide to the iron atom in methemoglobin is thought to be associated with increased planarity of the heme group and increased stability of the heme-globin complex. The stabilizing effect of cyanide in the above experiments suggests that Heinz body formation, heat precipitation of hemoglobin, and the increased alkali denaturation of methemoglobin depend on changes of heme-globin binding.
Images
PMCID: PMC322738  PMID: 5480860
24.  A Study of the Hydration of the Alkali Metal Ions in Aqueous Solution 
Inorganic Chemistry  2011;51(1):425-438.
The hydration of the alkali metal ions in aqueous solution has been studied by large angle X-ray scattering (LAXS) and double difference infrared spectroscopy (DDIR). The structures of the dimethyl sulfoxide solvated alkali metal ions in solution have been determined to support the studies in aqueous solution. The results of the LAXS and DDIR measurements show that the sodium, potassium, rubidium and cesium ions all are weakly hydrated with only a single shell of water molecules. The smaller lithium ion is more strongly hydrated, most probably with a second hydration shell present. The influence of the rubidium and cesium ions on the water structure was found to be very weak, and it was not possible to quantify this effect in a reliable way due to insufficient separation of the O–D stretching bands of partially deuterated water bound to these metal ions and the O–D stretching bands of the bulk water. Aqueous solutions of sodium, potassium and cesium iodide and cesium and lithium hydroxide have been studied by LAXS and M–O bond distances have been determined fairly accurately except for lithium. However, the number of water molecules binding to the alkali metal ions is very difficult to determine from the LAXS measurements as the number of distances and the temperature factor are strongly correlated. A thorough analysis of M–O bond distances in solid alkali metal compounds with ligands binding through oxygen has been made from available structure databases. There is relatively strong correlation between M–O bond distances and coordination numbers also for the alkali metal ions even though the M–O interactions are weak and the number of complexes of potassium, rubidium and cesium with well-defined coordination geometry is very small. The mean M–O bond distance in the hydrated sodium, potassium, rubidium and cesium ions in aqueous solution have been determined to be 2.43(2), 2.81(1), 2.98(1) and 3.07(1) Å, which corresponds to six-, seven-, eight- and eight-coordination. These coordination numbers are supported by the linear relationship of the hydration enthalpies and the M–O bond distances. This correlation indicates that the hydrated lithium ion is four-coordinate in aqueous solution. New ionic radii are proposed for four- and six-coordinate lithium(I), 0.60 and 0.79 Å, respectively, as well as for five- and six-coordinate sodium(I), 1.02 and 1.07 Å, respectively. The ionic radii for six- and seven-coordinate K+, 1.38 and 1.46 Å, respectively, and eight-coordinate Rb+ and Cs+, 1.64 and 1.73 Å, respectively, are confirmed from previous studies. The M–O bond distances in dimethyl sulfoxide solvated sodium, potassium, rubidium and cesium ions in solution are very similar to those observed in aqueous solution.
The hydration of alkali metal ions has been studied by large angle X-ray scattering, LAXS, and double difference infrared spectroscopy. The obtained M−O bond distances from LAXS have been compared to relevant crystal structures, conclusions about hydration numbers in aqueous solution have been made, and new ionic radii have been proposed. Hydration numbers of six, seven, eight and eight are proposed for the sodium, potassium, rubidium and cesium ions in aqueous solution.
doi:10.1021/ic2018693
PMCID: PMC3250073  PMID: 22168370
25.  Long-lasting inhibition of presynaptic metabolism and neurotransmitter release by protein S-nitrosylation 
Free radical biology & medicine  2010;49(5):757-769.
Nitric oxide (NO) and related reactive nitrogen species (RNS) play a major role in the pathophysiology of stroke and other neurodegenerative diseases. One of the poorly understood consequences of stroke is a long-lasting inhibition of synaptic transmission. In this study, we tested the hypothesis that RNS can produce long-term inhibition of neurotransmitter release via S-nitrosylation of proteins in presynaptic nerve endings. We examined the effects of exogenous sources of RNS on the vesicular and non-vesicular L-[3H]glutamate release from rat brain synaptosomes. NO/RNS donors, such as spermine NONOate, MAHMA NONOate, S-nitroso-L-cysteine, and SIN-1, inhibited only the vesicular component of glutamate release with the order of potency that closely matched levels of protein S-nitrosylation. Inhibition of glutamate release persisted for >1 hr after RNS donor decomposition and wash out, and strongly correlated with decreases in the intrasynaptosomal ATP levels. Post-NO treatment of synaptosomes with thiol-reducing reagents decreased the total content of S-nitrosylated proteins but had little effect on glutamate release and ATP levels. In contrast, post-NO application of the end-product of glycolysis pyruvate partially rescued neurotransmitter release and ATP production. These data suggest that RNS suppress presynaptic metabolism and neurotransmitter release via poorly reversible modifications of glycolytic and mitochondrial enzymes, one of which was identified as glyceraldehyde-3-phosphate dehydrogenase. Similar mechanism may contribute to the long-term suppression of neuronal communication during nitrosative stress in vivo.
doi:10.1016/j.freeradbiomed.2010.05.032
PMCID: PMC2923826  PMID: 20633346
nitric oxide; S-nitroso-L-cysteine; S-nitrosylation; S-nitrosation; neurotransmitter release; energetic metabolism; brain

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