Experts and Doctors on molecular models in Singapore, Central Singapore, Singapore


Locale: Singapore, Central Singapore, Singapore
Topic: molecular models

Top Publications

  1. Bhunia A, Domadia P, Xu X, Gingras R, Ni F, Bhattacharjya S. Equilibrium unfolding of the dimeric SAM domain of MAPKKK Ste11 from the budding yeast: role of the interfacial residues in structural stability and binding. Biochemistry. 2008;47:651-9 pubmed
    ..These results demonstrate that the interfacial residues of the dimeric SAM domain of Ste11 are critically involved in its structural stability and binding to the Ste50 SAM domain. ..
  2. Virshup D, Shenolikar S. From promiscuity to precision: protein phosphatases get a makeover. Mol Cell. 2009;33:537-45 pubmed publisher
    ..As recent publications illustrate, these regulatory subunits confer specificity, selectivity, localization, and regulation on these important enzymes. ..
  3. Doley R, Kini R. Protein complexes in snake venom. Cell Mol Life Sci. 2009;66:2851-71 pubmed publisher
    ..Here, we describe the structure and function of various protein complexes of snake venoms and their role in snake venom toxicity. ..
  4. Dastidar S, Lane D, Verma C. Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100. BMC Bioinformatics. 2009;10 Suppl 15:S6 pubmed publisher
    ..The mobility of this residue can be modulated by the conformations of p53 and the Nterminal lid region of MDM2. ..
  5. Liu Q, Li J. Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective. BMC Bioinformatics. 2010;11:244 pubmed publisher
    ..It can be noted that DWE bicliques, especially the unique bicliques, can capture deep insights into the binding characteristics of protein interfaces. ..
  6. Rishikesan S, Manimekalai M, Gruber G. The NMR solution structure of subunit G (G(61)(-)(101)) of the eukaryotic V1VO ATPase from Saccharomyces cerevisiae. Biochim Biophys Acta. 2010;1798:1961-8 pubmed publisher
    ..Together with the recently determined NMR solution structure of G(1)(-)(59), the presented solution structure of G(61)(-)(101) enabled us to present a first structural model of the entire subunit G of the S. cerevisiae V(1)V(O) ATPase. ..
  7. Yap K, Liu X, Thenmozhiyal J, Ho P. Characterization of the 13-cis-retinoic acid/cyclodextrin inclusion complexes by phase solubility, photostability, physicochemical and computational analysis. Eur J Pharm Sci. 2005;25:49-56 pubmed
    ..The results showed that HP-beta-CD was a proper excipient for increasing solubility and stability of 13-cis-RA. ..
  8. Lu L, Tai G, Wu M, Song H, Hong W. Multilayer interactions determine the Golgi localization of GRIP golgins. Traffic. 2006;7:1399-407 pubmed
    ..This third tier of interaction with the membrane could be mediated by non-specific hydrophobic and electrostatic forces. ..
  9. Liew C, Sharff A, Kotaka M, Kong R, Sun H, Qureshi I, et al. Induced-fit upon ligand binding revealed by crystal structures of the hot-dog fold thioesterase in dynemicin biosynthesis. J Mol Biol. 2010;404:291-306 pubmed publisher

More Information

Publications146 found, 100 shown here

  1. Chong C, Tan L, Lim L, Manser E. The mechanism of PAK activation. Autophosphorylation events in both regulatory and kinase domains control activity. J Biol Chem. 2001;276:17347-53 pubmed
    ..Thus two autophosphorylation sites direct activation while three others control association with focal complexes via PIX and Nck. ..
  2. Tan I, Seow K, Lim L, Leung T. Intermolecular and intramolecular interactions regulate catalytic activity of myotonic dystrophy kinase-related Cdc42-binding kinase alpha. Mol Cell Biol. 2001;21:2767-78 pubmed
    ..We therefore suggest that binding of phorbol ester to MRCK releases its autoinhibition, allowing N-terminal dimerization and subsequent kinase activation. ..
  3. Wang C, Balasubramanian M, Dokland T. Structure, crystal packing and molecular dynamics of the calponin-homology domain of Schizosaccharomyces pombe Rng2. Acta Crystallogr D Biol Crystallogr. 2004;60:1396-403 pubmed
    ..This distinctive feature is absent from previously published CH-domain structures. Another feature revealed by comparing the two derivatives is the presence of two loop conformations between Tyr92 and Arg99. ..
  4. Qin H, Noberini R, Huan X, Shi J, Pasquale E, Song J. Structural characterization of the EphA4-Ephrin-B2 complex reveals new features enabling Eph-ephrin binding promiscuity. J Biol Chem. 2010;285:644-54 pubmed publisher
    ..Our findings shed light on the distinctive features that enable the remarkable ligand binding promiscuity of EphA4 and suggest that diverse strategies are needed to effectively disrupt different Eph-ephrin complexes. ..
  5. Davey G, Wu B, Dong Y, Surana U, Davey C. DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent. Nucleic Acids Res. 2010;38:2081-8 pubmed publisher
  6. Tan S, Hugo W, Sung W, Ng S. A correlated motif approach for finding short linear motifs from protein interaction networks. BMC Bioinformatics. 2006;7:502 pubmed
    ..This, in turn, will expedite the discovery of novel linear binding motifs, and facilitate the studies of biological pathways mediated by them. ..
  7. Brown C, Srinivasan D, Jun L, Coomber D, Verma C, Lane D. The electrostatic surface of MDM2 modulates the specificity of its interaction with phosphorylated and unphosphorylated p53 peptides. Cell Cycle. 2008;7:608-10 pubmed
    ..In agreement with computational predictions, the binding to phosphorylated p53 peptide, in comparison to the unphosphorylated p53 peptide, was enhanced upon mutation of 3 key residues on the MDM2 surface. ..
  8. Sunita S, Tkaczuk K, Purta E, Kasprzak J, Douthwaite S, Bujnicki J, et al. Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J Mol Biol. 2008;383:652-66 pubmed publisher
  9. Li X, Ng M, Wang Y, Zhou T, Chua S, Yuan W, et al. Site-specific self-cleavage of G-quadruplexes formed by human telemetric repeats. Bioorg Med Chem Lett. 2008;18:5576-80 pubmed publisher
    ..Our further studies verify that these reactions are site-specific and undergo hydrolytic pathways. ..
  10. Tan Y, Chan S, Ong T, Yit L, Tiong Y, Chew F, et al. Structures of two major allergens, Bla g 4 and Per a 4, from cockroaches and their IgE binding epitopes. J Biol Chem. 2009;284:3148-57 pubmed publisher
    ..A major IgE binding epitope unique to Per a 4 is found on the loops at the bottom of the beta-barrel that may aid the development of hypoallergens for immunotherapy...
  11. Kumar A, Manimekalai M, Balakrishna A, Jeyakanthan J, Gruber G. Nucleotide binding states of subunit A of the A-ATP synthase and the implication of P-loop switch in evolution. J Mol Biol. 2010;396:301-20 pubmed publisher
  12. Long D, Yang D. Millisecond timescale dynamics of human liver fatty acid binding protein: testing of its relevance to the ligand entry process. Biophys J. 2010;98:3054-61 pubmed publisher
    ..Furthermore, we suggest these results show that the ligand-entry related functional dynamics could occur on the microsecond/submicrosecond timescales, highly encouraging future computational studies on this topic. ..
  13. Vasudevan D, Chua E, Davey C. Crystal structures of nucleosome core particles containing the '601' strong positioning sequence. J Mol Biol. 2010;403:1-10 pubmed publisher
    ..Our findings indicate that DNA stretching is an intrinsically predisposed site-specific property of the nucleosome and suggest how NCP crystal structures with diverse DNA sequences can be obtained. ..
  14. Kumar A, Manimekalai M, Balakrishna A, Priya R, Biukovic G, Jeyakanthan J, et al. The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding. J Mol Biol. 2010;401:892-905 pubmed publisher
    ..Taken together, the data presented demonstrate the concerted effects of the critical residues P235A, F236, and S238 in the unique P-loop conformation of the A-ATP synthases. ..
  15. Verma C, Fischer S. Protein stability and ligand binding: new paradigms from in-silico experiments. Biophys Chem. 2005;115:295-302 pubmed
  16. Liu J, Li M, Ran X, Fan J, Song J. Structural insight into the binding diversity between the human Nck2 SH3 domains and proline-rich proteins. Biochemistry. 2006;45:7171-84 pubmed
    ..Interestingly, of the three SH3-binding motifs carried by Wrch1, only the middle one was capable of binding SH3-2. Our results provide valuable clues for further functional investigations into the Nck2-mediated signaling networks. ..
  17. Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki J, et al. Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein. PLoS ONE. 2007;2:e548 pubmed
    ..However, phylogenetic analysis suggests that all type II AFPs evolved from the common ancestor and developed different ice-binding modes. We clarify the evolutionary relationship of type II AFPs to sugar-binding lectins. ..
  18. Kurabachew M, Lu S, Krastel P, Schmitt E, Suresh B, Goh A, et al. Lipiarmycin targets RNA polymerase and has good activity against multidrug-resistant strains of Mycobacterium tuberculosis. J Antimicrob Chemother. 2008;62:713-9 pubmed publisher
    ..Furthermore, rifampicin-resistant strains remained fully susceptible to lipiarmycin, and none of the lipiarmycin-resistant MTB strains became resistant to rifampicin, highlighting the lack of cross-resistance. ..
  19. Chen H, Yang J, Lin C, Yuan Y. Structural basis for RNA-silencing suppression by Tomato aspermy virus protein 2b. EMBO Rep. 2008;9:754-60 pubmed publisher
    ..Biochemical experiments suggest that TAV2b might interfere with the post-transcriptional gene silencing pathway by directly binding to siRNA duplex. ..
  20. Kang C, Hong Y, Dhe Paganon S, Yoon H. FKBP family proteins: immunophilins with versatile biological functions. Neurosignals. 2008;16:318-25 pubmed publisher
    ..This review focuses on molecular characteristics of the canonical and noncanonical FKBP family members and the biological functions of their ligands in performing neuroprotective and neurotrophic activities. ..
  21. Yu L, Yu P, Yee Yen Mui E, McKelvie J, Pham T, Yap Y, et al. Phage display screening against a set of targets to establish peptide-based sugar mimetics and molecular docking to predict binding site. Bioorg Med Chem. 2009;17:4825-32 pubmed publisher
    ..Of the three cyclic peptides subjected to computational docking, CNTPLTSRC had the highest predicted affinity and CSRILTAAC demonstrated specificity for the sugar binding site comparable to the natural ligand itself. ..
  22. Mavinahalli J, Madhumalar A, Beuerman R, Lane D, Verma C. Differences in the transactivation domains of p53 family members: a computational study. BMC Genomics. 2010;11 Suppl 1:S5 pubmed publisher
    ..Phosphorylations of the peptides further modulate the stability of the helix and control associations with partner proteins. ..
  23. Biukovic G, Rössle M, Gayen S, Mu Y, Gruber G. Small-angle X-ray scattering reveals the solution structure of the peripheral stalk subunit H of the A1AO ATP synthase from Methanocaldococcus jannaschii and its binding to the catalytic A subunit. Biochemistry. 2007;46:2070-8 pubmed
    ..Tryptophan emission spectra showed specific binding of H and H8-104 to the neighboring, catalytic A subunit, which could not be detected in the presence of H1-98. Finally, the arrangement of H within the A1AO ATP synthase is presented. ..
  24. Lin C, Yuan Y. Structural insights into histone H3 lysine 56 acetylation by Rtt109. Structure. 2008;16:1503-10 pubmed publisher
    ..We have further proposed the unique H3-K56 anchoring pocket and the potential H3alphaN binding groove. Our work has provided structural insights to understand the acetylation mechanism of H3-K56 by Rtt109. ..
  25. Qin H, Shi J, Noberini R, Pasquale E, Song J. Crystal structure and NMR binding reveal that two small molecule antagonists target the high affinity ephrin-binding channel of the EphA4 receptor. J Biol Chem. 2008;283:29473-84 pubmed publisher
    ..Furthermore, the results demonstrate that the high affinity ephrin binding channel of the Eph receptors is amenable to targeting with small molecule antagonists and suggest avenues for further optimization. ..
  26. Hernandez Valladares M, Kim T, Kannan B, Tung A, Aguda A, Larsson M, et al. Structural characterization of a capping protein interaction motif defines a family of actin filament regulators. Nat Struct Mol Biol. 2010;17:497-503 pubmed publisher
    ..Peptides comprising these CPI motifs are able to inhibit CP and to uncap CP-bound actin filaments. ..
  27. Alag R, Qureshi I, Bharatham N, Shin J, Lescar J, Yoon H. NMR and crystallographic structures of the FK506 binding domain of human malarial parasite Plasmodium vivax FKBP35. Protein Sci. 2010;19:1577-86 pubmed publisher
  28. Xu H, Tai J, Ye H, Kang C, Yoon H. The N-terminal domain of tumor suppressor p53 is involved in the molecular interaction with the anti-apoptotic protein Bcl-Xl. Biochem Biophys Res Commun. 2006;341:938-44 pubmed
    ..Taken together, our data suggest that p53NTD interacts with Bcl-Xl but the characteristic of the molecular interaction appears to be different from that of the DNA-binding domain of p53. ..
  29. Gruber G, Marshansky V. New insights into structure-function relationships between archeal ATP synthase (A1A0) and vacuolar type ATPase (V1V0). Bioessays. 2008;30:1096-109 pubmed publisher
    ..This review will summarize the current knowledge on the structure, mechanism and regulation of A-ATP synthases and V-ATPases. The importance of V-ATPase in pathophysiology of diseases will be discussed. ..
  30. Huang S, Chua J, Yew W, Sivaraman J, Moore P, Tan C, et al. Site-directed mutagenesis on human cystathionine-gamma-lyase reveals insights into the modulation of H2S production. J Mol Biol. 2010;396:708-18 pubmed publisher
  31. Low B, Seow K, Guy G. The BNIP-2 and Cdc42GAP homology domain of BNIP-2 mediates its homophilic association and heterophilic interaction with Cdc42GAP. J Biol Chem. 2000;275:37742-51 pubmed
    ..The results suggest that BCH domains of BNIP-2 and Cdc42GAP represent a novel protein-protein interaction domain that could potentially determine and/or modify the physiological roles of these molecules. ..
  32. Pervushin K, Tan E, Parthasarathy K, Lin X, Jiang F, Yu D, et al. Structure and inhibition of the SARS coronavirus envelope protein ion channel. PLoS Pathog. 2009;5:e1000511 pubmed publisher
    ..The channel structure presented herein provides a possible rationale for inhibition, and a platform for future structure-based drug design of this potential pharmacological target. ..
  33. Chua H, Jois S, Sim M, Go M. Transport of angiotensin peptides across the Caco-2 monolayer. Peptides. 2004;25:1327-38 pubmed
    ..On the other hand, the more hydrophilic angiotensin IV had less hydrogen bonding potential and a solution conformation characterized by a beta turn. These factors may influence the transport characteristics of DAAI and angiotensin IV. ..
  34. Yang Y, Lyubartsev A, Korolev N, Nordenskiöld L. Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles. Biophys J. 2009;96:2082-94 pubmed publisher
    ..A more detailed description of the NCP did not change the main features of the results. Overall, the results of this work are in agreement with experimental data reported for NCP solutions and for chromatin arrays...
  35. Vithana E, Morgan P, Ramprasad V, Tan D, Yong V, Venkataraman D, et al. SLC4A11 mutations in Fuchs endothelial corneal dystrophy. Hum Mol Genet. 2008;17:656-66 pubmed
  36. Ling S, Decker C, Walsh M, She M, Parker R, Song H. Crystal structure of human Edc3 and its functional implications. Mol Cell Biol. 2008;28:5965-76 pubmed publisher
  37. Liu P, Sudhaharan T, Koh R, Hwang L, Ahmed S, Maruyama I, et al. Investigation of the dimerization of proteins from the epidermal growth factor receptor family by single wavelength fluorescence cross-correlation spectroscopy. Biophys J. 2007;93:684-98 pubmed
    ..These receptors are major targets of anti-cancer drug development, and the receptors' homo- and heterodimeric structures are relevant for such developments. ..
  38. Loh P, Yang H, Walsh M, Wang Q, Wang X, Cheng Z, et al. Structural basis for translational inhibition by the tumour suppressor Pdcd4. EMBO J. 2009;28:274-85 pubmed publisher
    ..Our structural and mutational analyses reveal that Pdcd4 inhibits translation initiation by trapping eIF4A in an inactive conformation, and blocking its incorporation into the eIF4F complex. ..
  39. Hu Z, Jiang J. Separation of amino acids in glucose isomerase crystal: insight from molecular dynamics simulations. J Chromatogr A. 2009;1216:5122-9 pubmed publisher
    ..The simulation results provide useful microscopic insight into the retention mechanisms in chromatographic separation process and suggest that glucose isomerase crystal has the capability to separate amino acids. ..
  40. Chow J, Wu L, Yew W. Directed evolution of a quorum-quenching lactonase from Mycobacterium avium subsp. paratuberculosis K-10 in the amidohydrolase superfamily. Biochemistry. 2009;48:4344-53 pubmed publisher
  41. Chen L, Muhlrad D, Hauryliuk V, Cheng Z, Lim M, Shyp V, et al. Structure of the Dom34-Hbs1 complex and implications for no-go decay. Nat Struct Mol Biol. 2010;17:1233-40 pubmed publisher
    ..Consistent with this role, NGD at runs of arginine codons, which cause a strong block to elongation, is independent of the Dom34-Hbs1 complex. ..
  42. Madhumalar A, Smith D, Verma C. Stability of the core domain of p53: insights from computer simulations. BMC Bioinformatics. 2008;9 Suppl 1:S17 pubmed publisher
  43. Xu C, Ng S, Chan H. Self-assembly of perfunctionalized beta-cyclodextrins on a quartz crystal microbalance for real-time chiral recognition. Langmuir. 2008;24:9118-24 pubmed publisher
    ..This study contributes to the realization of novel chiral sensors applicable for real-time recognition and analysis of enantiomeric alcohols and lactates. ..
  44. Gan S, Ng L, Lin X, Gong X, Torres J. Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain. Protein Sci. 2008;17:813-20 pubmed publisher
    ..We provide a model for this pore, which should be useful in mutagenesis studies to elucidate its role during the virus cycle. ..
  45. Sun Q, Collins R, Huang S, Holmberg Schiavone L, Anand G, Tan C, et al. Structural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S. J Biol Chem. 2009;284:3076-85 pubmed publisher
    ..These results provide significant insights, which will facilitate the structure-based design of novel inhibitors of hCSE to aid in the development of therapies for diseases involving disorders of sulfur metabolism. ..
  46. Chen B, Fang S, Tam J, Liu D. Formation of stable homodimer via the C-terminal alpha-helical domain of coronavirus nonstructural protein 9 is critical for its function in viral replication. Virology. 2009;383:328-37 pubmed publisher
    ..Introduction of these mutations into the viral genome showed only mild to moderate effects on the growth and infectivity of the rescued mutant viruses. ..
  47. Husain N, Tkaczuk K, Tulsidas S, Kaminska K, Cubrilo S, Maravic Vlahovicek G, et al. Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases. Nucleic Acids Res. 2010;38:4120-32 pubmed publisher
    ..This analysis can serve as a stepping stone towards developing drugs that would specifically block the activity of Arm methyltransferases and thereby re-sensitize pathogenic bacteria to aminoglycoside antibiotics. ..
  48. Zhang Z, Lee H, Mihalek I. Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity. BMC Bioinformatics. 2010;11:155 pubmed publisher
  49. Sim H, Lee C, Ee P, Go M. Dimethoxyaurones: Potent inhibitors of ABCG2 (breast cancer resistance protein). Eur J Pharm Sci. 2008;35:293-306 pubmed publisher
    ..Thus, functionalized 4,6-dimethoxyaurones are promising ABCG2 inhibitors that combine good activity at submicromolar concentrations with limited antiproliferative activity. ..
  50. Yeo C, Tham J, Yap M, Poh C. Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): entrapment in plasmid RP4 and sequence analysis. Microbiology. 1997;143 ( Pt 8):2833-40 pubmed
    ..This is the first reported group II intron isolated from Pseudomonas spp. and the first time that the mobility of a bacterial group II intron has been demonstrated. ..
  51. Hong W. SNAREs and traffic. Biochim Biophys Acta. 2005;1744:120-44 pubmed
    ..In the post-genomic era, a fairly complete list of "all" SNAREs in several organisms (including human) can now be made. This review aims to summarize the key properties and the mechanism of action of SNAREs in mammalian cells. ..
  52. She M, Decker C, Svergun D, Round A, Chen N, Muhlrad D, et al. Structural basis of dcp2 recognition and activation by dcp1. Mol Cell. 2008;29:337-49 pubmed publisher
    ..Notably, the interface of Dcp1 and Dcp2 is not fully conserved, explaining why the Dcp1-Dcp2 interaction in higher eukaryotes requires an additional factor. ..
  53. Yang S, Noble C, Yang D. Characterization of DLC1-SAM equilibrium unfolding at the amino acid residue level. Biochemistry. 2009;48:4040-9 pubmed publisher
    ..Analysis of the midpoints of the transitions shows that the unfolding of the native state and formation of the denatured state are not cooperative and the unfolding of only a few residues seems to follow a two-state mechanism. ..
  54. Wu B, Davey C. Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome. J Mol Biol. 2010;398:633-40 pubmed publisher
    ..This indicates that divalent metals and histone tails can both collaborate and compete in minor groove association, which sheds light on nucleosome solubility and chromatin compaction behavior. ..
  55. Bhunia A, Domadia P, Torres J, Hallock K, Ramamoorthy A, Bhattacharjya S. NMR structure of pardaxin, a pore-forming antimicrobial peptide, in lipopolysaccharide micelles: mechanism of outer membrane permeabilization. J Biol Chem. 2010;285:3883-95 pubmed publisher
    ..Saturation transfer difference NMR identifies residues of Pa4 that are intimately associated with LPS micelles. Collectively, our results provide mechanistic insights into the outer membrane permeabilization by pardaxin. ..
  56. Vararattanavech A, Chng C, Parthasarathy K, Tang X, Torres J, Tan S. A transmembrane polar interaction is involved in the functional regulation of integrin alpha L beta 2. J Mol Biol. 2010;398:569-83 pubmed publisher
    ..Our results provide an example of the stabilizing effect of polar interactions within the low dielectric environment of the membrane interior and demonstrate its importance in the regulation of alpha L beta 2 function. ..
  57. Xu Y, Seet L, Hanson B, Hong W. The Phox homology (PX) domain, a new player in phosphoinositide signalling. Biochem J. 2001;360:513-30 pubmed
  58. Zhang D, Li N, Lok S, Zhang L, Swaminathan K. Isomaltulose synthase (PalI) of Klebsiella sp. LX3. Crystal structure and implication of mechanism. J Biol Chem. 2003;278:35428-34 pubmed
    ..Selected C-terminal truncations have been shown to reduce and even abolish the enzyme activity, consistent with the predicted role of the C-terminal residues in the maintenance of enzyme conformation and active site topology. ..
  59. Palasingam P, Jauch R, Ng C, Kolatkar P. The structure of Sox17 bound to DNA reveals a conserved bending topology but selective protein interaction platforms. J Mol Biol. 2009;388:619-30 pubmed publisher
  60. Brown C, Dastidar S, See H, Coomber D, Ortiz Lombardia M, Verma C, et al. Rational design and biophysical characterization of thioredoxin-based aptamers: insights into peptide grafting. J Mol Biol. 2010;395:871-83 pubmed publisher
    ..These need to be sufficient to compensate for the destabilization of the scaffold by peptide insertion. These observations will be useful in future aptamer designs. ..
  61. Gayen S, Gruber G. Disulfide linkage in the coiled-coil domain of subunit H of A1AO ATP synthase from Methanocaldococcus jannaschii and the NMR structure of the C-terminal segment H(85-104). FEBS Lett. 2010;584:713-8 pubmed publisher
    ..Together with the surface charge distribution of H(85-104), these results shine light into the A-H assembly of this enzyme. ..
  62. Lim W, Feng Y. Applying the stochastic difference equation to DNA conformational transitions: a study of B-Z and B-A DNA transitions. Biopolymers. 2005;78:107-20 pubmed
    ..Qualitative features of the simulated B-A transition also agree well with experimental data. The SDEL approach is thus a suitable numerical technique to compute long-time molecular dynamics trajectory for DNA molecules. ..
  63. Fan Y, Chen X, Trigg A, Tung C, Kong J, Gao Z. Detection of MicroRNAs using target-guided formation of conducting polymer nanowires in nanogaps. J Am Chem Soc. 2007;129:5437-43 pubmed
    ..0 fM. The biosensor array is applied to the direct detection of miRNA in total RNA extracted from cancer cell lines. ..
  64. Thaker Y, Roessle M, Gruber G. The boxing glove shape of subunit d of the yeast V-ATPase in solution and the importance of disulfide formation for folding of this protein. J Bioenerg Biomembr. 2007;39:275-89 pubmed
    ..Cysteins, involved in disulfide bridges, were analyzed by MALDI-TOF mass spectrometry. Finally, the solution structure of subunit d will be discussed in terms of the topological arrangement of the V(1)V(O) ATPase. ..
  65. Wu M, Wang T, Loh E, Hong W, Song H. Structural basis for recruitment of RILP by small GTPase Rab7. EMBO J. 2005;24:1491-501 pubmed
    ..Structural comparison suggests that the combined use of RabSF1 and RabSF4 with the switch regions may be a general mode of action for most Rab proteins in regulating membrane trafficking. ..
  66. Schafer I, Rössle M, Biukovic G, Muller V, Gruber G. Structural and functional analysis of the coupling subunit F in solution and topological arrangement of the stalk domains of the methanogenic A1AO ATP synthase. J Bioenerg Biomembr. 2006;38:83-92 pubmed
    ..Based on these data the surface of contact of B-F could be mapped in the high-resolution structure of subunit B of the A(1)A(O) ATP synthase. ..
  67. Zhu Y, Ng P, Wang L, Ho B, Ding J. Diversity in lectins enables immune recognition and differentiation of wide spectrum of pathogens. Int Immunol. 2006;18:1671-80 pubmed
    ..The functional diversity of lectins in invertebrates appears to evolutionarily compensate for the lack of acquired immunity. ..
  68. Keller T, Chen Y, Knox J, Lim S, Ma N, Patel S, et al. Finding new medicines for flaviviral targets. Novartis Found Symp. 2006;277:102-14; discussion 114-9, 251-3 pubmed
    ..NS3 helicase can also be considered a viable drug target for flaviviral diseases. It has however proved to be a challenging for HCV and selectivity issues versus human helicases must be overcome. ..
  69. Gopalan G, Chopra S, Ranganathan A, Swaminathan K. Crystal structure of uncleaved L-aspartate-alpha-decarboxylase from Mycobacterium tuberculosis. Proteins. 2006;65:796-802 pubmed publisher
    ..coli ADC proenzyme structure. As pantothenate is synthesized in microorganisms, plants, and fungi but not in animals, structure elucidation of Mtb ADC is of substantial interest for structure-based drug development...
  70. Lin Z, Sriskanthadevan S, Huang H, Siu C, Yang D. Solution structures of the adhesion molecule DdCAD-1 reveal new insights into Ca(2+)-dependent cell-cell adhesion. Nat Struct Mol Biol. 2006;13:1016-22 pubmed publisher
    ..Our results provide new insights into Ca(2+)-dependent mechanisms for cell-cell adhesion...
  71. Noble C, Song H. Structural studies of elongation and release factors. Cell Mol Life Sci. 2008;65:1335-46 pubmed publisher
  72. Chua T, Bujnicki J, Tan T, Huynh F, Patel B, Sivaraman J. The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode. Plant Cell. 2008;20:1059-72 pubmed publisher
    ..orenii SPS. Our findings indicate that SPS from H. orenii may represent a valid model for the catalytic domain of plant SPSs and thus may provide useful insight into the reaction mechanism of the plant enzyme. ..
  73. Liu S, Zhou L, Chen L, Dastidar S, Verma C, Li J, et al. Effect of structural parameters of peptides on dimer formation and highly oxidized side products in the oxidation of thiols of linear analogues of human beta-defensin 3 by DMSO. J Pept Sci. 2009;15:95-106 pubmed publisher
    ..Together with molecular modelling, we propose a reaction mechanism to elucidate the oxidation results of these peptides. ..
  74. Mohideen K, Muhammad R, Davey C. Perturbations in nucleosome structure from heavy metal association. Nucleic Acids Res. 2010;38:6301-11 pubmed publisher
    ..Sustained binding and the ability to induce structural perturbations at specific locations in the nucleosome may contribute to genetic and epigenetic mechanisms of carcinogenesis mediated by Co(2+) and Ni(2+). ..
  75. Vithana E, Nongpiur M, Venkataraman D, Chan S, Mavinahalli J, Aung T. Identification of a novel mutation in the NTF4 gene that causes primary open-angle glaucoma in a Chinese population. Mol Vis. 2010;16:1640-5 pubmed
    ..Identification of a single mutation in our study suggests that NTF4 mutations are a rare cause of POAG (0.6%, 95%CI 0.02%-3.16%) in Chinese people. ..
  76. Manimekalai M, Kumar A, Balakrishna A, Gruber G. A second transient position of ATP on its trail to the nucleotide-binding site of subunit B of the motor protein A(1)A(0) ATP synthase. J Struct Biol. 2009;166:38-45 pubmed publisher
  77. Yang J, Peng Z, Chen X. Prediction of protein structural classes for low-homology sequences based on predicted secondary structure. BMC Bioinformatics. 2010;11 Suppl 1:S9 pubmed publisher
    ..Thus, it is a valuable method to predict protein structural classes particularly for low-homology amino acid sequences. ..
  78. Kini R. Structure-function relationships and mechanism of anticoagulant phospholipase A2 enzymes from snake venoms. Toxicon. 2005;45:1147-61 pubmed
    ..Thus, these studies strongly support the target model which suggests that protein-protein interaction rather than protein-phospholipid interaction determines the pharmacological specificity of PLA(2) enzymes...
  79. Hong W. SNAREs and traffic. Biochim Biophys Acta. 2005;1744:493-517 pubmed
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