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1.  Harnessing a Physiologic Mechanism for siRNA Delivery With Mimetic Lipoprotein Particles 
Molecular Therapy  2012;20(8):1582-1589.
Therapeutics based on RNA interference (RNAi) have emerged as a potential new class of drugs for treating human disease by silencing the target messenger RNA (mRNA), thereby reducing levels of the corresponding pathogenic protein. The major challenge for RNAi therapeutics is the development of safe delivery vehicles for small interfering RNAs (siRNAs). We previously showed that cholesterol-conjugated siRNAs (chol-siRNA) associate with plasma lipoprotein particles and distribute primarily to the liver after systemic administration to mice. We further demonstrated enhancement of silencing by administration of chol-siRNA pre-associated with isolated high-density lipoprotein (HDL) or low-density lipoprotein (LDL). In this study, we investigated mimetic lipoprotein particle prepared from recombinant apolipoprotein A1 (apoA) and apolipoprotein E3 (apoE) as a delivery vehicle for chol-siRNAs. We show that apoE-containing particle (E-lip) is highly effective in functional delivery of chol-siRNA to mouse liver. E-lip delivery was found to be considerably more potent than apoA-containing particle (A-lip). Furthermore, E-lip–mediated delivery was not significantly affected by high endogenous levels of plasma LDL. These results demonstrate that E-lip has substantial potential as delivery vehicles for lipophilic conjugates of siRNAs.
doi:10.1038/mt.2012.33
PMCID: PMC3412494  PMID: 22850721
2.  Serotonin-Induced Hypersensitivity via Inhibition of Catechol O-Methyltransferase Activity 
Molecular Pain  2012;8:25.
The subcutaneous and systemic injection of serotonin reduces cutaneous and visceral pain thresholds and increases responses to noxious stimuli. Different subtypes of 5-hydroxytryptamine (5-HT) receptors are suggested to be associated with different types of pain responses. Here we show that serotonin also inhibits catechol O-methyltransferase (COMT), an enzyme that contributes to modultion the perception of pain, via non-competitive binding to the site bound by catechol substrates with a binding affinity comparable to the binding affinity of catechol itself (Ki = 44 μM). Using computational modeling, biochemical tests and cellular assays we show that serotonin actively competes with the methyl donor S-adenosyl-L-methionine (SAM) within the catalytic site. Binding of serotonin to the catalytic site inhibits the access of SAM, thus preventing methylation of COMT substrates. The results of in vivo animal studies show that serotonin-induced pain hypersensitivity in mice is reduced by either SAM pretreatment or by the combined administration of selective antagonists for β2- and β3-adrenergic receptors, which have been previously shown to mediate COMT-dependent pain signaling. Our results suggest that inhibition of COMT via serotonin binding contributes to pain hypersensitivity, providing additional strategies for the treatment of clinical pain conditions.
doi:10.1186/1744-8069-8-25
PMCID: PMC3495668  PMID: 22500608
4.  Emergence of Protein Fold Families through Rational Design 
PLoS Computational Biology  2006;2(7):e85.
Diverse proteins with similar structures are grouped into families of homologs and analogs, if their sequence similarity is higher or lower, respectively, than 20%–30%. It was suggested that protein homologs and analogs originate from a common ancestor and diverge in their distinct evolutionary time scales, emerging as a consequence of the physical properties of the protein sequence space. Although a number of studies have determined key signatures of protein family organization, the sequence-structure factors that differentiate the two evolution-related protein families remain unknown. Here, we stipulate that subtle structural changes, which appear due to accumulating mutations in the homologous families, lead to distinct packing of the protein core and, thus, novel compositions of core residues. The latter process leads to the formation of distinct families of homologs. We propose that such differentiation results in the formation of analogous families. To test our postulate, we developed a molecular modeling and design toolkit, Medusa, to computationally design protein sequences that correspond to the same fold family. We find that analogous proteins emerge when a backbone structure deviates only 1–2 Å root-mean-square deviation from the original structure. For close homologs, core residues are highly conserved. However, when the overall sequence similarity drops to ~25%–30%, the composition of core residues starts to diverge, thereby forming novel families of protein homologs. This direct observation of the formation of protein homologs within a specific fold family supports our hypothesis. The conservation of amino acids in designed sequences recapitulates that of the naturally occurring sequences, thereby validating our computational design methodology.
Synopsis
Studies of known proteins have revealed intriguing co-organization of their sequences and structures. Proteins with sequence similarity higher than 25%–30% usually adopt a similar structure and are called homologs, whereas those with low sequence similarity (<20%) can share the same structure and are referred as analogs. The origin of such co-organization has been a topic of extensive discussions among protein folding, design, and evolution research communities, because understanding of the emergence of homologs and analogs in the protein universe has broad implications for our ability to rationally manipulate proteins. In this study, the authors developed a molecular modeling and design method, Medusa, to computationally design diversified protein sequences that correspond to similar backbone structures, which determine a protein fold family. Using Medusa, the authors directly demonstrated the formation of distinct protein homologs within a specific fold family when the structure deviates only 1–2 Å away from the original structure. The study suggests that subtle structural changes, which appear due to accumulating mutations in the families of homologs, lead to a distinct packing of the protein core and, thus, novel compositions of core residues. The latter process leads to the formation of distinct families of homologs.
doi:10.1371/journal.pcbi.0020085
PMCID: PMC1487181  PMID: 16839198
5.  Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases  
PLoS Computational Biology  2005;1(3):e30.
Expansion of polyglutamine (polyQ) tracts in proteins results in protein aggregation and is associated with cell death in at least nine neurodegenerative diseases. Disease age of onset is correlated with the polyQ insert length above a critical value of 35–40 glutamines. The aggregation kinetics of isolated polyQ peptides in vitro also shows a similar critical-length dependence. While recent experimental work has provided considerable insights into polyQ aggregation, the molecular mechanism of aggregation is not well understood. Here, using computer simulations of isolated polyQ peptides, we show that a mechanism of aggregation is the conformational transition in a single polyQ peptide chain from random coil to a parallel β-helix. This transition occurs selectively in peptides longer than 37 glutamines. In the β-helices observed in simulations, all residues adopt β-strand backbone dihedral angles, and the polypeptide chain coils around a central helical axis with 18.5 ± 2 residues per turn. We also find that mutant polyQ peptides with proline-glycine inserts show formation of antiparallel β-hairpins in their ground state, in agreement with experiments. The lower stability of mutant β-helices explains their lower aggregation rates compared to wild type. Our results provide a molecular mechanism for polyQ-mediated aggregation.
Synopsis
Nine human diseases, including Huntington's disease, are associated with an expanded trinucleotide sequence CAG in genes. Since CAG codes for the amino acid glutamine, these disorders are collectively known as polyglutamine diseases. Although the genes (and proteins) involved in different polyglutamine diseases have little in common, the disorders they cause follow a strikingly similar course: If the length of the expansion exceeds a critical value of 35–40, the greater the number of glutamine repeats in a protein, the earlier the onset of disease and the more severe the symptoms. This fact suggests that abnormally long glutamine tracts render their host protein toxic to nerve cells, and all polyglutamine diseases are hypothesized to progress via common molecular mechanisms. One possible mechanism of cell death is that the abnormally long sequence of glutamines acquires a shape that prevents the host protein from folding into its proper shape. What is the structure acquired by polyglutamine and what is the molecular basis of the observed threshold repeat length? Using computer models of polyglutamine, the authors show that if, and only if, the length of polyglutamine repeats is longer than the critical value found in disease, it acquires a specific shape called a β-helix. The longer the glutamine tract length, the higher is the propensity to form β-helices. This length-dependent formation of β-helices by polyglutamine stretches may provide a unified molecular framework for understanding the structural basis of different trinucleotide repeat-associated diseases.
doi:10.1371/journal.pcbi.0010030
PMCID: PMC1193989  PMID: 16158094

Results 1-5 (5)