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1.  MemPype: a pipeline for the annotation of eukaryotic membrane proteins 
Nucleic Acids Research  2011;39(Web Server issue):W375-W380.
MemPype is a Python-based pipeline including previously published methods for the prediction of signal peptides (SPEP), glycophosphatidylinositol (GPI) anchors (PredGPI), all-alpha membrane topology (ENSEMBLE), and a recent method (MemLoci) that specifically discriminates the localization of eukaryotic membrane proteins in: ‘cell membrane’, ‘internal membranes’, ‘organelle membranes’. MemLoci scores with accuracy of 70% and generalized correlation coefficient (GCC) of 0.50 on a rigorous homology-unbiased validation set and overpasses other predictors for subcellular localization. The annotation process is based both on inheritance through homology and computational methods. Each submitted protein first retrieves, when available, up to 25 similar proteins (with sequence identity ≥50% and alignment coverage ≥50% on both sequences). This helps the identification of membrane-associated proteins and detailed localization tags. Each protein is also filtered for the presence of a GPI anchor [0.8% false positive rate (FPR)]. A positive score of GPI anchor prediction labels the sequence as exposed to ‘Cell surface’. Concomitantly the sequence is analysed for the presence of a signal peptide and classified with MemLoci into one of three discriminated classes. Finally the sequence is filtered for predicting its putative all-alpha protein membrane topology (FPR <1%). The web server is available at: http://mu2py.biocomp.unibo.it/mempype.
doi:10.1093/nar/gkr282
PMCID: PMC3125734  PMID: 21543452
2.  CaV1.2 I-II linker structure and Timothy syndrome 
Channels  2012;6(6):468-472.
CaV channels are multi-subunit protein complexes that enable inward cellular Ca2+ currents in response to membrane depolarization. We recently described structure-function studies of the intracellular α1 subunit domain I-II linker, directly downstream of domain IS6. The results show the extent of the linker’s helical structure to be subfamily dependent, as dictated by highly conserved primary sequence differences. Moreover, the difference in structure confers different biophysical properties, particularly the extent and kinetics of voltage and calcium-dependent inactivation. Timothy syndrome is a human genetic disorder due to mutations in the CaV1.2 gene. Here, we explored whether perturbation of the I-II linker helical structure might provide a mechanistic explanation for a Timothy syndrome mutant’s (human CaV1.2 G406R equivalent) biophysical effects on inactivation and activation. The results are equivocal, suggesting that a full mechanistic explanation for this Timothy syndrome mutation requires further investigation.
doi:10.4161/chan.22078
PMCID: PMC3536733  PMID: 22990809
Timothy syndrome; voltage-dependent calcium channels; voltage-dependent inactivation; α-helix
3.  Development of a Multi-Channel Piezoelectric Acoustic Sensor Based on an Artificial Basilar Membrane 
Sensors (Basel, Switzerland)  2013;14(1):117-128.
In this research, we have developed a multi-channel piezoelectric acoustic sensor (McPAS) that mimics the function of the natural basilar membrane capable of separating incoming acoustic signals mechanically by their frequency and generating corresponding electrical signals. The McPAS operates without an external energy source and signal processing unit with a vibrating piezoelectric thin film membrane. The shape of the vibrating membrane was chosen to be trapezoidal such that different locations of membrane have different local resonance frequencies. The length of the membrane is 28 mm and the width of the membrane varies from 1 mm to 8 mm. Multiphysics finite element analysis (FEA) was carried out to predict and design the mechanical behaviors and piezoelectric response of the McPAS model. The designed McPAS was fabricated with a MEMS fabrication process based on the simulated results. The fabricated device was tested with a mouth simulator to measure its mechanical and piezoelectrical frequency response with a laser Doppler vibrometer and acoustic signal analyzer. The experimental results show that the as fabricated McPAS can successfully separate incoming acoustic signals within the 2.5 kHz–13.5 kHz range and the maximum electrical signal output upon acoustic signal input of 94 dBSPL was 6.33 mVpp. The performance of the fabricated McPAS coincided well with the designed parameters.
doi:10.3390/s140100117
PMCID: PMC3926549  PMID: 24361926
cochlea; piezoelectric; microelectromechanical system (MEMS); artificial basilar membrane (ABM); laser Doppler vibrometer (LDV)
4.  Caveolin-1 Contributes to Assembly of Store-operated Ca2+ Influx Channels by Regulating Plasma Membrane Localization of TRPC1 
The Journal of biological chemistry  2003;278(29):27208-27215.
TRPC1, a component of store-operated Ca2+ entry (SOCE) channels, is assembled in a complex with caveolin- 1 (Cav1) and key Ca2+ signaling proteins. This study examines the role of Cav1 in the function of TRPC1. TRPC1 and Cav1 were colocalized in the plasma membrane region of human submandibular gland and Madin-Darby canine kidney cells. Full-length Cav1 bound to both the N and C termini of TRPC1. Amino acids 271–349, which includes a Cav1 binding motif (amino acids 322–349), was identified as the Cav1 binding domain in the TRPC1 N terminus. Deletion of amino acids 271–349 or 322–349 prevented plasma membrane localization of TRPC1. Importantly, TRPC1Δ271–349 induced a dominant suppression of SOCE and was associated with wild-type TRPC1. Although the role of the C-terminal Cav1 binding domain is not known, its deletion did not affect localization of TRPC1 (Singh, B. B., Liu, X., and Ambudkar, I. S. (2000) J. Biol. Chem. 275, 36483–36486). Further, expression of a truncated Cav1 (Cav1Δ51–169), but not full-length Cav1, similarly disrupted plasma membrane localization of endogenously and exogenously expressed TRPC1 in human Submandibular gland and Madin-Darby canine kidney cells. Cav1Δ51–169 also suppressed thapsigargin- and carbachol-stimulated Ca2+ influx and increased the detergent solubility of TRPC1, although plasma membrane lipid raft domains were not disrupted. These data demonstrate that plasma membrane localization of TRPC1 depends on an interaction between its N terminus and Cav1. Thus, our data suggest that Cav1 has an important role in the assembly of SOCE channel(s).
doi:10.1074/jbc.M301118200
PMCID: PMC3621139  PMID: 12732636
5.  Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units 
PLoS Genetics  2006;2(4):e46.
Membrane organization describes the orientation of a protein with respect to the membrane and can be determined by the presence, or absence, and organization within the protein sequence of two features: endoplasmic reticulum signal peptides and alpha-helical transmembrane domains. These features allow protein sequences to be classified into one of five membrane organization categories: soluble intracellular proteins, soluble secreted proteins, type I membrane proteins, type II membrane proteins, and multi-spanning membrane proteins. Generation of protein isoforms with variable membrane organizations can change a protein's subcellular localization or association with the membrane. Application of MemO, a membrane organization annotation pipeline, to the FANTOM3 Isoform Protein Sequence mouse protein set revealed that within the 8,032 transcriptional units (TUs) with multiple protein isoforms, 573 had variation in their use of signal peptides, 1,527 had variation in their use of transmembrane domains, and 615 generated protein isoforms from distinct membrane organization classes. The mechanisms underlying these transcript variations were analyzed. While TUs were identified encoding all pairwise combinations of membrane organization categories, the most common was conversion of membrane proteins to soluble proteins. Observed within our high-confidence set were 156 TUs predicted to generate both extracellular soluble and membrane proteins, and 217 TUs generating both intracellular soluble and membrane proteins. The differential use of endoplasmic reticulum signal peptides and transmembrane domains is a common occurrence within the variable protein output of TUs. The generation of protein isoforms that are targeted to multiple subcellular locations represents a major functional consequence of transcript variation within the mouse transcriptome.
Synopsis
Many genes produce only a single protein; however, others are known to produce a number of proteins with different functions in the cell. The function of a protein within the cell is influenced by its location; for example, proteins that are secreted can act as messengers, whereas proteins embedded in the membrane may act as receptors or channels. Features that determine the eventual location of a protein are found in the protein sequence. The authors identified two such features, the signal peptide that targets a protein for secretion, and the transmembrane domain that embeds a protein in the membrane, predicting their occurrence in mouse protein sequences. The authors then searched the entire mouse genome for genes that vary in the use of these features in protein isoforms. They found a large number of genes that produce proteins with variation in these features; for example, they identified genes producing proteins that are both secreted and intracellular, and genes producing proteins that are both membrane bound and soluble. This process is likely to be a major source of functional variation in the output of mammalian genes.
doi:10.1371/journal.pgen.0020046
PMCID: PMC1449889  PMID: 16683029
6.  T-type channels buddy up 
Pflugers Archiv  2014;466:661-675.
The electrical output of neurons relies critically on voltage- and calcium-gated ion channels. The traditional view of ion channels is that they operate independently of each other in the plasma membrane in a manner that could be predicted according to biophysical characteristics of the isolated current. However, there is increasing evidence that channels interact with each other not just functionally but also physically. This is exemplified in the case of Cav3 T-type calcium channels, where new work indicates the ability to form signaling complexes with different types of calcium-gated and even voltage-gated potassium channels. The formation of a Cav3-K complex provides the calcium source required to activate KCa1.1 or KCa3.1 channels and, furthermore, to bestow a calcium-dependent regulation of Kv4 channels via associated KChIP proteins. Here, we review these interactions and discuss their significance in the context of neuronal firing properties.
doi:10.1007/s00424-013-1434-6
PMCID: PMC3951889  PMID: 24413887
Cav3; T-type; KCa3.1; KCa1.1; BK; Kv4; A-type
7.  Consequences of Stabilizing the Natively Disordered F helix for the Folding Pathway of Apomyoglobin 
Journal of molecular biology  2011;411(1):248-263.
The F helix region of sperm whale apomyoglobin (apoMb) is disordered, undergoing conformational fluctuations between a folded helical conformation and one or more locally unfolded states. In order to examine the effects of F helix stabilization on the folding pathway of apoMb, we have introduced mutations to augment intrinsic helical structure in the F helix of the kinetic folding intermediate and to increase its propensity to fold early in the pathway, using predictions based on plots of the average area buried upon folding (AABUF) derived from the primary sequence. Two mutant proteins were prepared, a double mutant P88K/S92K (F2) and a quadruple mutant, P88K/A90L/S92K/A94L (F4). Whereas the AABUF for F2 predicts that the F helix will not fold early in the pathway, the F helix in F4 shows a significantly increased AABUF and is therefore predicted to fold early. Protection of amide protons by formation of hydrogen-bonded helical structure during the early folding events has been analyzed by pH-pulse labeling. Consistent with the AABUF prediction, many of the F helix residues for F4 are significantly protected in the kinetic intermediate but are not protected in the F2 mutant. F4 folds via a kinetically trapped burst phase intermediate that contains stabilized secondary structure in the A, B, F, G, and H helix regions. Rapid folding of the F helix stabilizes the central core of the misfolded intermediate and inhibits translocation of the H helix back to its native position, thereby decreasing the overall folding rate.
doi:10.1016/j.jmb.2011.05.028
PMCID: PMC3143293  PMID: 21640124
site-directed mutagenesis; NMR; protein folding; hydrogen-deuterium exchange; quench-flow pulse labeling
8.  Understanding the physical properties controlling protein crystallization based on analysis of large-scale experimental data 
Nature biotechnology  2009;27(1):51-57.
Crystallization has proven to be the most significant bottleneck to high-throughput protein structure determination using diffraction methods. We have used the large-scale, systematically generated experimental results of the Northeast Structural Genomics Consortium to characterize the biophysical properties that control protein crystallization. Datamining of crystallization results combined with explicit folding studies lead to the conclusion that crystallization propensity is controlled primarily by the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. These analyses identify specific sequence features correlating with crystallization propensity that can be used to estimate the crystallization probability of a given construct. Analyses of entire predicted proteomes demonstrate substantial differences in the bulk amino acid sequence properties of human versus eubacterial proteins that reflect likely differences in their biophysical properties including crystallization propensity. Finally, our thermodynamic measurements enable critical evaluation of previous claims regarding correlations between protein stability and bulk sequence properties, which generally are not supported by our dataset.
doi:10.1038/nbt.1514
PMCID: PMC2746436  PMID: 19079241
protein crystallization; protein thermodynamics; crystallization mechanism; surface entropy; datamining; structural genomics
9.  Biophysics of α-Synuclein Membrane Interactions 
Biochimica et Biophysica Acta  2011;1818(2):162-171.
Membrane proteins participate in nearly all cellular processes; however, because of experimental limitations, their characterization lags far behind that of soluble proteins. Peripheral membrane proteins are particularly challenging to study because of their inherent propensity to adopt multiple and/or transient conformations in solution and upon membrane association. In this review, we summarize useful biophysical techniques for the study of peripheral membrane proteins and their application in the characterization of the membrane interactions of the natively unfolded and Parkinson’s disease (PD) related protein, α-synuclein (α-syn). We give particular focus to studies that have led to the current understanding of membrane-bound α-syn structure and the elucidation of specific membrane properties that affect α-syn-membrane binding. Finally, we discuss biophysical evidence supporting a key role for membranes and α-syn in PD pathogenesis.
doi:10.1016/j.bbamem.2011.07.032
PMCID: PMC3249522  PMID: 21819966
10.  Molecular mechanisms in signal transduction at the membrane 
Signal transduction originates at the membrane, where the clustering of signaling proteins is a key step in transmitting a message. Membranes are difficult to study, and their influence on signaling is still only understood at the most rudimentary level. Recent advances in the biophysics of membranes, surveyed in this review, have highlighted a variety of phenomena that are likely to influence signaling activity, such as local composition heterogeneities and long-range mechanical effects. We discuss recent mechanistic insights into three signaling systems—Ras activation, Ephrin signaling and the control of actin nucleation—where the active role of membrane components is now appreciated and for which experimentation on the membrane is required for further understanding.
doi:10.1038/nsmb.1844
PMCID: PMC3703790  PMID: 20495561
11.  A Hidden Markov Model method, capable of predicting and discriminating β-barrel outer membrane proteins 
BMC Bioinformatics  2004;5:29.
Background
Integral membrane proteins constitute about 20–30% of all proteins in the fully sequenced genomes. They come in two structural classes, the α-helical and the β-barrel membrane proteins, demonstrating different physicochemical characteristics, structure and localization. While transmembrane segment prediction for the α-helical integral membrane proteins appears to be an easy task nowadays, the same is much more difficult for the β-barrel membrane proteins. We developed a method, based on a Hidden Markov Model, capable of predicting the transmembrane β-strands of the outer membrane proteins of gram-negative bacteria, and discriminating those from water-soluble proteins in large datasets. The model is trained in a discriminative manner, aiming at maximizing the probability of correct predictions rather than the likelihood of the sequences.
Results
The training has been performed on a non-redundant database of 14 outer membrane proteins with structures known at atomic resolution; it has been tested with a jacknife procedure, yielding a per residue accuracy of 84.2% and a correlation coefficient of 0.72, whereas for the self-consistency test the per residue accuracy was 88.1% and the correlation coefficient 0.824. The total number of correctly predicted topologies is 10 out of 14 in the self-consistency test, and 9 out of 14 in the jacknife. Furthermore, the model is capable of discriminating outer membrane from water-soluble proteins in large-scale applications, with a success rate of 88.8% and 89.2% for the correct classification of outer membrane and water-soluble proteins respectively, the highest rates obtained in the literature. That test has been performed independently on a set of known outer membrane proteins with low sequence identity with each other and also with the proteins of the training set.
Conclusion
Based on the above, we developed a strategy, that enabled us to screen the entire proteome of E. coli for outer membrane proteins. The results were satisfactory, thus the method presented here appears to be suitable for screening entire proteomes for the discovery of novel outer membrane proteins. A web interface available for non-commercial users is located at: , and it is the only freely available HMM-based predictor for β-barrel outer membrane protein topology.
doi:10.1186/1471-2105-5-29
PMCID: PMC385222  PMID: 15070403
12.  Membrane Topology and Insertion of Membrane Proteins: Search for Topogenic Signals 
Integral membrane proteins are found in all cellular membranes and carry out many of the functions that are essential to life. The membrane-embedded domains of integral membrane proteins are structurally quite simple, allowing the use of various prediction methods and biochemical methods to obtain structural information about membrane proteins. A critical step in the biosynthetic pathway leading to the folded protein in the membrane is its insertion into the lipid bilayer. Understanding of the fundamentals of the insertion and folding processes will significantly improve the methods used to predict the three-dimensional membrane protein structure from the amino acid sequence. In the first part of this review, biochemical approaches to elucidate membrane protein topology are reviewed and evaluated, and in the second part, the use of similar techniques to study membrane protein insertion is discussed. The latter studies search for signals in the polypeptide chain that direct the insertion process. Knowledge of the topogenic signals in the nascent chain of a membrane protein is essential for the evaluation of membrane topology studies.
PMCID: PMC98984  PMID: 10704472
13.  Molecular regulations governing TREK and TRAAK channel functions 
Channels  2011;5(5):402-409.
K+ channels with two-pore domain (K2p) form a large family of hyperpolarizing channels. They produce background currents that oppose membrane depolarization and cell excitability. They are involved in cellular mechanisms of apoptosis, vasodilatation, anesthesia, pain, neuroprotection and depression. This review focuses on TREK-1, TREK-2 and TRAAK channels subfamily and on the mechanisms that contribute to their molecular heterogeneity and functional regulations. Not only the number of genes determines their molecular diversity but also by alternative splicing and alternative initiation of translation. These channels are sensitive to a wide array of biophysical parameters that affect their activity such as unsaturated fatty acids, intra- and extracellular pH, membrane stretch, temperature and intracellular signaling pathways. They interact with partner proteins that influence their activity and their plasma membrane expression. Molecular heterogeneity, regulatory mechanisms and protein partners are all expected to contribute to cell specific functions of TREK currents in many tissues.
doi:10.4161/chan.5.5.16469
PMCID: PMC3265763  PMID: 21829087
background K+ channels; K2p; TREK-TRAAK; molecular regulations
14.  Identification of outer membrane proteins of Mycobacterium tuberculosis 
SUMMARY
The cell wall of mycobacteria contains an unusual outer membrane of extremely low permeability. While Escherichia coli uses more than 60 proteins to functionalize its outer membrane, only two mycobacterial outer membrane proteins (OMPs) are known. The porin MspA of Mycobacterium smegmatis provided the proof of principle that integral mycobacterial OMPs share the β-barrel structure, the absence of hydrophobic α-helices and the presence of a signal peptide with OMPs of gram-negative bacteria. These properties were exploited in a multi-step bioinformatic approach to predict OMPs of M. tuberculosis. A secondary structure analysis was performed for 587 proteins of M. tuberculosis predicted to be exported. Scores were calculated for the β-strand content and the amphiphilicity of the β-strands. Reference OMPs of gram-negative bacteria defined threshold values for these parameters that were met by 144 proteins of unknown function of M. tuberculosis. Two of them were verified as OMPs of unknown functions by a novel two-step experimental approach. Rv1698 and Rv1973 were detected only in the total membrane fraction of M. bovis BCG in Western blot experiments, while proteinase K digestion of whole cells showed the surface accessibility of these proteins. These findings established that Rv1698 and Rv1973 are indeed localized in the outer membrane and tripled the number of known OMPs of M. tuberculosis. Significantly, these results provide evidence for the usefulness of the bioinformatic approach to predict mycobacterial OMPs and indicate that M. tuberculosis likely has many OMPs with β-barrel structure. Our findings pave the way to identify the set of proteins which functionalize the outer membrane of M. tuberculosis.
doi:10.1016/j.tube.2008.02.004
PMCID: PMC2615007  PMID: 18439872
secondary structure; prediction; amphiphilicity; beta-strand; exported; inner membrane; periplasmic; secreted proteins
15.  CaMKII-Based Regulation of Voltage-Gated Na+ Channel in Cardiac Disease 
Circulation  2012;126(17):10.1161/CIRCULATIONAHA.112.105320.
Background
Human gene variants affecting ion channel biophysical activity and/or membrane localization are linked with potentially fatal cardiac arrhythmias. However, the mechanism for many human arrhythmia variants remains undefined despite over a decade of investigation. Post-translational modulation of membrane proteins is essential for normal cardiac function. Importantly, aberrant myocyte signaling has been linked to defects in cardiac ion channel post-translational modifications and disease. We recently identified a novel pathway for post-translational regulation of the primary cardiac voltage-gated Na+ channel (Nav1.5) by CaMKII. However, a role for this pathway in cardiac disease has not been evaluated.
Methods and Results
We evaluated the role of CaMKII-dependent phosphorylation in human genetic and acquired disease. We report an unexpected link between a short motif in the Nav1.5 DI-DII loop, recently shown to be critical for CaMKII-dependent phosphorylation, and Nav1.5 function in monogenic arrhythmia and common heart disease. Experiments in heterologous cells and primary ventricular cardiomyocytes demonstrate that human arrhythmia susceptibility variants (A572D and Q573E) alter CaMKII-dependent regulation of Nav1.5 resulting in abnormal channel activity and cell excitability. In silico analysis reveals that these variants functionally mimic the phosphorylated channel resulting in increased susceptibility to arrhythmia-triggering afterdepolarizations. Finally, we report that this same motif is aberrantly regulated in a large animal model of acquired heart disease and in failing human myocardium.
Conclusions
We identify the mechanism for two human arrhythmia variants that affect Nav1.5 channel activity through direct effects on channel post-translational modification. We propose that the CaMKII phosphorylation motif in the Nav1.5 DI-DII cytoplasmic loop is a critical nodal point for pro-arrhythmic changes to Nav1.5 in congenital and acquired cardiac disease.
doi:10.1161/CIRCULATIONAHA.112.105320
PMCID: PMC3811023  PMID: 23008441
arrhythmia (mechanisms); calmodulin dependent protein kinase II; heart failure; ion channels; long-QT syndrome; myocardial infarction
16.  Take home lessons from studies of related proteins 
Highlights
► We review the recent advances made from the study of related proteins. ► We relate pathway malleability to the balance between foldons and helical propensity. ► We speculate why different topologies respond differently to mutation. ► We discuss the role of kinetic intermediates in folding pathways. ► We explain why it is important to study several members from each protein fold.
The ‘Fold Approach’ involves a detailed analysis of the folding of several topologically, structurally and/or evolutionarily related proteins. Such studies can reveal determinants of the folding mechanism beyond the gross topology, and can dissect the residues required for folding from those required for stability or function. While this approach has not yet matured to the point where we can predict the native conformation of any polypeptide chain in silico, it has been able to highlight, amongst others, the specific residues that are responsible for nucleation, pathway malleability, kinetic intermediates, chain knotting, internal friction and Paracelsus switches. Some of the most interesting discoveries have resulted from the attempt to explain differences between homologues.
doi:10.1016/j.sbi.2012.11.009
PMCID: PMC3578095  PMID: 23265640
17.  MemBrain: Improving the Accuracy of Predicting Transmembrane Helices 
PLoS ONE  2008;3(6):e2399.
Prediction of transmembrane helices (TMH) in α helical membrane proteins provides valuable information about the protein topology when the high resolution structures are not available. Many predictors have been developed based on either amino acid hydrophobicity scale or pure statistical approaches. While these predictors perform reasonably well in identifying the number of TMHs in a protein, they are generally inaccurate in predicting the ends of TMHs, or TMHs of unusual length. To improve the accuracy of TMH detection, we developed a machine-learning based predictor, MemBrain, which integrates a number of modern bioinformatics approaches including sequence representation by multiple sequence alignment matrix, the optimized evidence-theoretic K-nearest neighbor prediction algorithm, fusion of multiple prediction window sizes, and classification by dynamic threshold. MemBrain demonstrates an overall improvement of about 20% in prediction accuracy, particularly, in predicting the ends of TMHs and TMHs that are shorter than 15 residues. It also has the capability to detect N-terminal signal peptides. The MemBrain predictor is a useful sequence-based analysis tool for functional and structural characterization of helical membrane proteins; it is freely available at http://chou.med.harvard.edu/bioinf/MemBrain/.
doi:10.1371/journal.pone.0002399
PMCID: PMC2396505  PMID: 18545655
18.  Prm3p Is a Pheromone-induced Peripheral Nuclear Envelope Protein Required for Yeast Nuclear Fusion 
Molecular Biology of the Cell  2009;20(9):2438-2450.
Nuclear membrane fusion is the last step in the mating pathway of the yeast Saccharomyces cerevisiae. We adapted a bioinformatics approach to identify putative pheromone-induced membrane proteins potentially required for nuclear membrane fusion. One protein, Prm3p, was found to be required for nuclear membrane fusion; disruption of PRM3 caused a strong bilateral defect, in which nuclear congression was completed but fusion did not occur. Prm3p was localized to the nuclear envelope in pheromone-responding cells, with significant colocalization with the spindle pole body in zygotes. A previous report, using a truncated protein, claimed that Prm3p is localized to the inner nuclear envelope. Based on biochemistry, immunoelectron microscopy and live cell microscopy, we find that functional Prm3p is a peripheral membrane protein exposed on the cytoplasmic face of the outer nuclear envelope. In support of this, mutations in a putative nuclear localization sequence had no effect on full-length protein function or localization. In contrast, point mutations and deletions in the highly conserved hydrophobic carboxy-terminal domain disrupted both protein function and localization. Genetic analysis, colocalization, and biochemical experiments indicate that Prm3p interacts directly with Kar5p, suggesting that nuclear membrane fusion is mediated by a protein complex.
doi:10.1091/mbc.E08-10-0987
PMCID: PMC2675623  PMID: 19297527
19.  The Compartmentalized Bacteria of the Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum Have Membrane Coat-Like Proteins 
PLoS Biology  2010;8(1):e1000281.
Compartmentalized bacteria have proteins that are structurally related to eukaryotic membrane coats, and one of these proteins localizes at the membrane of vesicles formed inside bacterial cells.
The development of the endomembrane system was a major step in eukaryotic evolution. Membrane coats, which exhibit a unique arrangement of β-propeller and α-helical repeat domains, play key roles in shaping eukaryotic membranes. Such proteins are likely to have been present in the ancestral eukaryote but cannot be detected in prokaryotes using sequence-only searches. We have used a structure-based detection protocol to search all proteomes for proteins with this domain architecture. Apart from the eukaryotes, we identified this protein architecture only in the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum, many members of which share a compartmentalized cell plan. We determined that one such protein is partly localized at the membranes of vesicles formed inside the cells in the planctomycete Gemmata obscuriglobus. Our results demonstrate similarities between bacterial and eukaryotic compartmentalization machinery, suggesting that the bacterial PVC superphylum contributed significantly to eukaryogenesis.
Author Summary
Despite decades of research, the origin of eukaryotic cells remains an unsolved issue. The endomembrane system defines the eukaryotic cell, and its origin is linked to that of eukaryotes. A search was conducted within all known sequences for proteins that are characteristic of the eukaryotic endomembrane system, using a combination of fold types that is uniquely found in the membrane coat proteins. Outside eukaryotes, such proteins were solely found in the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum. By immuno-electron microscopy, one of these bacterial proteins was found to localize adjacent to the membranes of vesicles found within the cells of one member of the PVC superphylum. Thus, there appear to be similarities between bacterial and eukaryotic compartmentalization systems, suggesting that the bacterial PVC superphylum may have contributed significantly to eukaryogenesis.
doi:10.1371/journal.pbio.1000281
PMCID: PMC2799638  PMID: 20087413
20.  HARMONY: a server for the assessment of protein structures 
Nucleic Acids Research  2006;34(Web Server issue):W231-W234.
Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (φ,ψ) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at
doi:10.1093/nar/gkl314
PMCID: PMC1538917  PMID: 16844999
21.  Characterization of the Molecular Architecture of Human Caveolin-3 and Interaction with the Skeletal Muscle Ryanodine Receptor* 
The Journal of Biological Chemistry  2012;287(48):40302-40316.
Background: Caveolin-3 facilitates both caveolae formation and a range of cell signaling pathways, including Ca2+ homeostasis.
Results: Caveolin-3 forms a disc-shaped nonamer that binds the Ca2+-release channel, RyR1.
Conclusion: Multiple caveolin-3 nonamers bind to a single RyR1 homotetramer.
Significance: First three-dimensional structural insights into caveolin-3 assembly, interactions with RyR1 suggest a novel role in muscle contraction and/or for channel localization within the membrane.
Caveolin-3 (cav-3), an integral membrane protein, is a building block of caveolae as well as a regulator of a number of physiological processes by facilitating the formation of multiprotein signaling complexes. We report that the expression of cav-3 in insect (Sf9) cells induces caveola formation, comparable in size with those observed in native tissue. We have also purified the recombinant cav-3 determining that it forms an oligomer of ∼220 kDa. We present the first three-dimensional structure for cav-3 (using transmission electron microscopy and single particle analysis methods) and show that nine cav-3 monomers assemble to form a complex that is toroidal in shape, ∼16.5 nm in diameter and ∼ 5.5 nm in height. Labeling experiments and reconstitution of the purified cav-3 into liposomes have allowed a proposal for the orientation of the protein with respect to the membrane. We have identified multiple caveolin-binding motifs within the ryanodine receptor (RyR1) sequence employing a bioinformatic analysis. We have then shown experimentally that there is a direct interaction between recombinant cav-3 nonamers and purified RyR1 homotetramers that would imply that at least one of the predicted cav-3-binding sites is exposed within the fully assembled RyR1 structure. The cav-3 three-dimensional model provides new insights as to how a cav-3 oligomer can bind multiple partners in close proximity to form signaling complexes. Furthermore, a direct interaction with RyR1 suggests a possible role for cav-3 as a modifier of muscle excitation-contraction coupling and/or for localization of the receptor to regions of the sarcoplasmic reticulum.
doi:10.1074/jbc.M112.377085
PMCID: PMC3504746  PMID: 23071107
Caveolae; Caveolin; Electron Microscopy (EM); Excitation-Contraction Coupling; Membrane Proteins; Muscle; Ryanodine Receptor; Sarcoplasmic Reticulum (SR); Scaffold Proteins; Single Particle Analysis
22.  Dynamin-driven membrane fission reveals catalytic principle of membrane remodeling 
Science (New York, N.Y.)  2013;339(6126):1433-1436.
Biological membrane fission is conducted by protein-driven stress. To create such membrane stress the GTPase dynamin-1, protein orchestrating membrane fission in endocytosis, assembles into helical scaffolds that constrict the necks of endocytic vesicles. We found that under constant GTP turnover two-rung dynamin scaffold is sufficient to produce fission of lipid nanotubes. Analyzing membrane fission by short dynamin scaffolds, we reveal a catalytic cycle which translates constriction stresses into fission. Upon constriction, coordinated membrane wedging by the scaffold facilitates reversible merger of the inner leaflet of the nanotube, the hemifission. Modeling of this reversible step identifies a low-energy path based on geometric coupling of the scaffold and the membrane. The final translation of the metastable hemifission into complete fission is stochastically linked to disassembly of the scaffold. This catalytic conversion of localized stresses into membrane remodeling suggests a novel paradigm for fission and fusion of cellular membranes.
doi:10.1126/science.1233920
PMCID: PMC3980720  PMID: 23520112
23.  LOCATE: a mouse protein subcellular localization database 
Nucleic Acids Research  2005;34(Database issue):D213-D217.
We present here LOCATE, a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set. Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing >1700 peer-reviewed publications. LOCATE represents the first effort to catalogue the experimentally verified subcellular location and membrane organization of mammalian proteins using a high-throughput approach and provides localization data for ∼40% of the mouse proteome. It is available at .
doi:10.1093/nar/gkj069
PMCID: PMC1347432  PMID: 16381849
24.  Understanding integration of α-helical membrane proteins: the next steps 
Trends in biochemical sciences  2012;37(8):303-308.
Integration of a protein into the endoplasmic reticulum (ER) membrane occurs through a series of multi-step reactions that include targeting of ribosome-nascent polypeptide complexes to the ER, attachment of the ribosome to the protein translocation channel, lateral partitioning of α-helical transmembrane spans into the lipid bilayer, and folding of the lumenal, cytosolic and membrane embedded domains of the protein. However, the molecular mechanisms and kinetics of these steps are still not entirely clear. To obtain a better understanding of the mechanism of membrane protein integration, we propose that it will be important to utilize in vivo experiments to examine the kinetics of membrane protein integration and in vitro experiments to characterize interactions between nascent membrane proteins, protein translocation factors and molecular chaperones.
doi:10.1016/j.tibs.2012.05.003
PMCID: PMC3557837  PMID: 22748693
25.  HIV-1 Assembly at the Plasma Membrane: Gag Trafficking and Localization 
Future virology  2009;4(3):241-257.
Virus particle formation of HIV-1 is a multi-step process driven by a viral structural protein Gag. This process takes place at the plasma membrane in most cell types. However, the pathway that directs Gag to the plasma membrane has recently come under intense scrutiny because of its importance in production of progeny virions as well as virus transmission at cell-cell contacts. This review highlights recent advances in our current understanding of mechanisms that traffic and localize Gag to the plasma membrane. In addition, findings on Gag association with specific plasma membrane domains are discussed in light of potential roles in cell-to-cell transmission.
doi:10.2217/fvl.09.4
PMCID: PMC2676728  PMID: 19802344
Plasma membrane; Gag; virus assembly; endosomal trafficking; late endosome/multivesicular body; membrane microdomain; membrane raft; tetraspanin; virological synapse; phosphatidylinositol-(4; 5)-bisphosphate

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