Genomes and Genes
Experts and Doctors on molecular models in Toronto, Ontario, Canada
Locale: Toronto, Ontario, Canada
Topic: molecular models
Publications107 found, 100 shown here
- Li G, Zhang Y, Chan M, Mal T, Hoeflich K, Inouye M, et al. Characterization of dual substrate binding sites in the homodimeric structure of Escherichia coli mRNA interferase MazF. J Mol Biol. 2006;357:139-50 pubmed
- Gonzalez C, Proudfoot M, Brown G, Korniyenko Y, Mori H, Savchenko A, et al. Molecular basis of formaldehyde detoxification. Characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J Biol Chem. 2006;281:14514-22 pubmed..Thus, FrmB and YeiG are S-formylglutathione hydrolases with a Ser-His-Asp catalytic triad involved in the detoxification of formaldehyde in E. coli. ..
- Qiu W, Wernimont A, Tang K, Taylor S, Lunin V, Schapira M, et al. Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii. EMBO J. 2009;28:969-79 pubmed publisher..This novel means of regulation governs ROP kinases implicated in parasite virulence. ..
- Velyvis A, Schachman H, Kay L. Application of methyl-TROSY NMR to test allosteric models describing effects of nucleotide binding to aspartate transcarbamoylase. J Mol Biol. 2009;387:540-7 pubmed publisher..These results indicate that the mechanism of action of ATP and CTP can be explained fully by the MWC model and that any scheme invoking structural changes of the c-chains is not correct. ..
- Orlicky S, Tang X, Neduva V, Elowe N, Brown E, Sicheri F, et al. An allosteric inhibitor of substrate recognition by the SCF(Cdc4) ubiquitin ligase. Nat Biotechnol. 2010;28:733-7 pubmed publisher..Mammalian WD40 domain proteins may exhibit similar allosteric responsiveness and hence represent an extensive class of druggable target. ..
- Asahi M, Green N, Kurzydlowski K, Tada M, MacLennan D. Phospholamban domain IB forms an interaction site with the loop between transmembrane helices M6 and M7 of sarco(endo)plasmic reticulum Ca2+ ATPases. Proc Natl Acad Sci U S A. 2001;98:10061-6 pubmed..These results suggest that a SERCA1-PLN interaction site occurs between L67 of SERCA1a and domain IB of PLN, which involves SERCA1a D813 and PLN N27 and N30. ..
- Soltyk A, Mackenzie C, Wolski V, Hirama T, Kitov P, Bundle D, et al. A mutational analysis of the globotriaosylceramide-binding sites of verotoxin VT1. J Biol Chem. 2002;277:5351-9 pubmed..Our data show that the interaction of verotoxin with the Gb(3) trisaccharide is highly context dependent and that a membrane environment is required for biologically relevant studies of the interaction. ..
- Overduin M, Harvey T, Bagby S, Tong K, Yau P, Takeichi M, et al. Solution structure of the epithelial cadherin domain responsible for selective cell adhesion. Science. 1995;267:386-9 pubmed..Unexpected structural similarities with the immunoglobulin fold suggest an evolutionary relation between calcium-dependent and calcium-independent cell adhesion molecules. ..
- Tollinger M, Crowhurst K, Kay L, Forman Kay J. Site-specific contributions to the pH dependence of protein stability. Proc Natl Acad Sci U S A. 2003;100:4545-50 pubmed..These interactions include a hydrogen bond between the Asp-8 side-chain and the Lys-21 backbone amide group in the folded state, which represents a highly conserved interaction in Src homology 3 domains. ..
- Wiesner S, Ogunjimi A, Wang H, Rotin D, Sicheri F, Wrana J, et al. Autoinhibition of the HECT-type ubiquitin ligase Smurf2 through its C2 domain. Cell. 2007;130:651-62 pubmed..Thus, interactions between C2 and HECT domains autoinhibit a subset of HECT-type E3s to protect them and their substrates from futile degradation in cells. ..
- Pell L, Gasmi Seabrook G, MORAIS M, Neudecker P, Kanelis V, Bona D, et al. The solution structure of the C-terminal Ig-like domain of the bacteriophage ? tail tube protein. J Mol Biol. 2010;403:468-79 pubmed publisher..Bioinformatics analyses have identified two conserved clusters of residues on the surface of gpV(C) that may be important in mediating the function of this domain...
- Nicholson B, White K. Context-influenced cap-independent translation of Tombusvirus mRNAs in vitro. Virology. 2008;380:203-12 pubmed publisher..These results reveal the contrasting activities of different TBSV-like 3'CITEs in vitro and shed light on the nature of the defect in TBSV. ..
- Cardarelli L, Lam R, Tuite A, Baker L, Sadowski P, Radford D, et al. The crystal structure of bacteriophage HK97 gp6: defining a large family of head-tail connector proteins. J Mol Biol. 2010;395:754-68 pubmed publisher..We have also identified gp7 of HK97 as a homologue of gp16 of phage SPP1, which is the second component of the connector of this phage. These proteins are members of another large protein family involved in connector assembly. ..
- Stollar E, Garcia B, Chong P, Rath A, Lin H, Forman Kay J, et al. Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p. J Biol Chem. 2009;284:26918-27 pubmed publisher..Our data imply that the AbpSH3 must bind extended target sites to function efficiently inside the cell. ..
- White A, Tull D, Johns K, Withers S, Rose D. Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase. Nat Struct Biol. 1996;3:149-54 pubmed..The active-site architecture of this covalent intermediate gives insights into both the classical double-displacement catalytic mechanism and the basis for the enzyme's specificity...
- Harrison A, Young A, Schnoelzer M, Paizs B. Formation of iminium ions by fragmentation of a2 ions. Rapid Commun Mass Spectrom. 2004;18:1635-40 pubmed..The experimental results are interpreted in terms of these energetics data, unimolecular rate constants calculated by using the RRKM theory, and the imine proton affinities. ..
- Orlicky S, Tang X, Willems A, Tyers M, Sicheri F. Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase. Cell. 2003;112:243-56 pubmed..These features account for the observed phosphorylation threshold in Sic1 recognition and suggest an equilibrium binding mode between a single receptor site in Cdc4 and multiple low-affinity CPD sites in Sic1. ..
- Viola C, Saridakis V, Christendat D. Crystal structure of chorismate synthase from Aquifex aeolicus reveals a novel beta alpha beta sandwich topology. Proteins. 2004;54:166-9 pubmed
- Julien J, Huarte N, Maeso R, Taneva S, Cunningham A, Nieva J, et al. Ablation of the complementarity-determining region H3 apex of the anti-HIV-1 broadly neutralizing antibody 2F5 abrogates neutralizing capacity without affecting core epitope binding. J Virol. 2010;84:4136-47 pubmed publisher..The present data therefore imply an extended 2F5 paratope that includes weak secondary interactions that are crucial for neutralization of Env-mediated fusion. ..
- Zwahlen C, Li S, Kay L, Pawson T, Forman Kay J. Multiple modes of peptide recognition by the PTB domain of the cell fate determinant Numb. EMBO J. 2000;19:1505-15 pubmed..Our results suggest a mechanism through which a single PTB domain might interact with multiple distinct target proteins to control a complex biological process such as asymmetric cell division. ..
- Wu B, Yee A, Huang Y, Ramelot T, Cort J, Semesi A, et al. The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain. Protein Sci. 2008;17:583-8 pubmed publisher..S17E bears a conserved positively charged surface acting as a robust scaffold for molecular recognition. The structure of M. thermoautotrophicum S17E provides a template for homology modeling of eukaryotic S17E proteins in the family...
- Fatemi N, Sarkar B. Structural and functional insights of Wilson disease copper-transporting ATPase. J Bioenerg Biomembr. 2002;34:339-49 pubmed
- Seet B, Berry D, Maltzman J, Shabason J, Raina M, Koretzky G, et al. Efficient T-cell receptor signaling requires a high-affinity interaction between the Gads C-SH3 domain and the SLP-76 RxxK motif. EMBO J. 2007;26:678-89 pubmed
- Rajakulendran T, Sahmi M, Lefrancois M, Sicheri F, Therrien M. A dimerization-dependent mechanism drives RAF catalytic activation. Nature. 2009;461:542-5 pubmed publisher..Together, our data identify the side-to-side dimer interface of RAF as a potential therapeutic target for intervention in BRAF-dependent tumorigenesis. ..
- Sarkari F, La Delfa A, Arrowsmith C, Frappier L, Sheng Y, Saridakis V. Further insight into substrate recognition by USP7: structural and biochemical analysis of the HdmX and Hdm2 interactions with USP7. J Mol Biol. 2010;402:825-37 pubmed publisher..These results lead to a better understanding of the mechanism of substrate recognition by USP7-NTD. ..
- Nagar B, Jones R, Diefenbach R, Isenman D, Rini J. X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2. Science. 1998;280:1277-81 pubmed..The structure supports a model whereby the transition of native C3 to its functionally active state involves the disruption of a complementary domain interface and provides insight into the basis for the interaction between C3d and CR2. ..
- Lim C, Seet B, Ingham R, Gish G, Matskova L, Winberg G, et al. The K15 protein of Kaposi's sarcoma-associated herpesvirus recruits the endocytic regulator intersectin 2 through a selective SH3 domain interaction. Biochemistry. 2007;46:9874-85 pubmed publisher..The ability of K15 to associate with ITSN2 suggests a new role for the K15 viral protein in intracellular protein trafficking...
- Feher M, Williams C. Effect of input differences on the results of docking calculations. J Chem Inf Model. 2009;49:1704-14 pubmed publisher..It is concluded that for the purposes of reproducibility and optimal performance, the most prudent procedure is to use multiple input structures for docking. The implications of these results on docking validation studies are discussed. ..
- Wernimont A, Artz J, Finerty P, Lin Y, Amani M, Allali Hassani A, et al. Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium. Nat Struct Mol Biol. 2010;17:596-601 pubmed publisher..This large conformational change constitutes a distinct mechanism in calcium signal-transduction pathways...
- Choi I, White K. An RNA activator of subgenomic mRNA1 transcription in tomato bushy stunt virus. J Biol Chem. 2002;277:3760-6 pubmed..These data are most consistent with a role for this interaction in regulating sg mRNA1 accumulation at the level of transcription. ..
- Yee A, Chang X, Pineda Lucena A, Wu B, Semesi A, Le B, et al. An NMR approach to structural proteomics. Proc Natl Acad Sci U S A. 2002;99:1825-30 pubmed publisher..Twelve structures are reported here as part of this approach, which allowed us to infer putative functions for several conserved hypothetical proteins...
- Slon Usakiewicz J, Ng W, Foster J, Dai J, Deretey E, Toledo Sherman L, et al. Frontal affinity chromatography with MS detection of EphB2 tyrosine kinase receptor. 1. Comparison with conventional ELISA. J Med Chem. 2004;47:5094-100 pubmed
- Min J, Allali Hassani A, Nady N, Qi C, Ouyang H, Liu Y, et al. L3MBTL1 recognition of mono- and dimethylated histones. Nat Struct Mol Biol. 2007;14:1229-30 pubmed..An unexpected mode of peptide-mediated dimerization suggests a possible mechanism for chromatin compaction by L3MBTL1. ..
- Avvakumov G, Walker J, Xue S, Li Y, Duan S, Bronner C, et al. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1. Nature. 2008;455:822-5 pubmed publisher..The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG. ..
- Aviv T, Lin Z, Lau S, Rendl L, Sicheri F, Smibert C. The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Nat Struct Biol. 2003;10:614-21 pubmed..Together, these results suggest that Smaug and Vts1 define a larger class of post-transcriptional regulators that act in part through a common transcript-recognition mechanism. ..
- Walsh P, Simonetti K, Sharpe S. Core structure of amyloid fibrils formed by residues 106-126 of the human prion protein. Structure. 2009;17:417-26 pubmed publisher..The close intermolecular contacts observed in the fibril core provide a rational for the sequence-dependent behavior of PrP(106-126), and provide a basis for further investigation of its biological properties. ..
- Fairn G, Ogata K, Botelho R, Stahl P, Anderson R, De Camilli P, et al. An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis. J Cell Biol. 2009;187:701-14 pubmed publisher..We conclude that a bistable electrostatic switch mechanism regulates the association/dissociation of PIP5Ks from the membrane during phagocytosis and likely other processes. ..
- Pineda Lucena A, Liao J, Wu B, Yee A, Cort J, Kennedy M, et al. NMR structure of the hypothetical protein encoded by the YjbJ gene from Escherichia coli. Proteins. 2002;47:572-4 pubmed
- Savchenko A, Skarina T, Evdokimova E, Watson J, Laskowski R, Arrowsmith C, et al. X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution. Proteins. 2004;54:162-5 pubmed
- Lee J, Singh V, Evans G, Tyler P, Furneaux R, Cornell K, et al. Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. J Biol Chem. 2005;280:18274-82 pubmed..Distance analysis of the nucleophile and leaving group show that MT-ImmA is a mimic of an early transition state, while MT-DADMe-ImmA is a better mimic of the highly dissociated transition state of E. coli MTAN. ..
- Vallurupalli P, Kay L. Complementarity of ensemble and single-molecule measures of protein motion: a relaxation dispersion NMR study of an enzyme complex. Proc Natl Acad Sci U S A. 2006;103:11910-5 pubmed
- Proudfoot M, Sanders S, Singer A, Zhang R, Brown G, Binkowski A, et al. Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain. J Mol Biol. 2008;375:301-15 pubmed..We suggest that, in vivo, some Zn ribbon domains might also bind iron and therefore possess an electron carrier activity, adding another physiological role to this large family of important proteins. ..
- Chow A, Ferrier Pages C, Khalouei S, Reynaud S, Brown I. Increased light intensity induces heat shock protein Hsp60 in coral species. Cell Stress Chaperones. 2009;14:469-76 pubmed publisher..This supports a correlation between stress induction of Hsp60 and (a) ability to counter perturbation of photosynthetic capacity by light and heat stress and (b) resistance to environmentally induced coral bleaching. ..
- Turner M, Yuan C, Borchardt R, Hershfield M, Smith G, Howell P. Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength. Nat Struct Biol. 1998;5:369-76 pubmed..An unusual dual role for a catalytic water molecule in the active site is revealed in the complex with the adenosine analog 2'-hydroxy, 3'-ketocyclopent-4'-enyladenine. ..
- Tugarinov V, Kay L. Quantitative NMR studies of high molecular weight proteins: application to domain orientation and ligand binding in the 723 residue enzyme malate synthase G. J Mol Biol. 2003;327:1121-33 pubmed..Some structural implications of the chemical shift perturbations upon binding and the estimated ligand on-rates are discussed. ..
- Donaldson L, Wojtyra U, Houry W. Solution structure of the dimeric zinc binding domain of the chaperone ClpX. J Biol Chem. 2003;278:48991-6 pubmed..However, the dimeric ZBD structure is not related to any protein structure in the Protein Data Bank. A trimer-of-dimers model of ZBD is presented, which might reflect the closed state of the ClpX hexamer. ..
- Qiu L, Pashkova N, Walker J, Winistorfer S, Allali Hassani A, Akutsu M, et al. Structure and function of the PLAA/Ufd3-p97/Cdc48 complex. J Biol Chem. 2010;285:365-72 pubmed publisher..These data suggest that the p97-PLAA interaction is important for a subset of PLAA-dependent biological processes and provides a framework to better understand the role of these complex molecules in the ubiquitin system. ..
- Henry P, Kanelis V, O Brien M, Kim B, Gautschi I, Forman Kay J, et al. Affinity and specificity of interactions between Nedd4 isoforms and the epithelial Na+ channel. J Biol Chem. 2003;278:20019-28 pubmed..Collectively, these results suggest that high affinity of WW domain-PY-motif interactions rather than affiliation with Nedd4-1/Nedd-2 is critical for ENaC suppression by Nedd4 proteins. ..
- Tsai M, Sampaleanu L, Greene C, Creagh L, Haynes C, Howell P. A duck delta1 crystallin double loop mutant provides insight into residues important for argininosuccinate lyase activity. Biochemistry. 2004;43:11672-82 pubmed
- Ghetu A, Corcoran C, Cerchietti L, Bardwell V, Melnick A, Prive G. Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer. Mol Cell. 2008;29:384-91 pubmed publisher..Mutations of critical BCOR(BBD) residues cause the disruption of the BCL6 corepression activities of BCOR, and a BCOR(BBD) peptide blocks BCL6-mediated transcriptional repression and kills lymphoma cells. ..
- Chan K, O Brien P. Structure-activity relationships for hepatocyte toxicity and electrophilic reactivity of alpha,beta-unsaturated esters, acrylates and methacrylates. J Appl Toxicol. 2008;28:1004-15 pubmed publisher..These results suggest that differences in hepatocyte toxicity of acrylates and methacrylates can be related to their electrophilic reactivity which corresponds to their ability to deplete GSH and protein thiols...
- Lau W, Baker L, Rubinstein J. Cryo-EM structure of the yeast ATP synthase. J Mol Biol. 2008;382:1256-64 pubmed publisher..This new map has allowed construction of a model of subunit arrangement in the F(O) motor of ATP synthase that dictates how dimerization of the complex via subunits e and g might occur. ..
- Wang F, Marshall C, Yamamoto K, Li G, Plevin M, You H, et al. Biochemical and structural characterization of an intramolecular interaction in FOXO3a and its binding with p53. J Mol Biol. 2008;384:590-603 pubmed publisher..We also show that p53 disrupts the intramolecular interaction between FH and CR3. These results provide evidence for interplay of the FH and CR3 domains in association with p53. ..
- Sampaleanu L, Bonanno J, Ayers M, Koo J, Tammam S, Burley S, et al. Periplasmic domains of Pseudomonas aeruginosa PilN and PilO form a stable heterodimeric complex. J Mol Biol. 2009;394:143-59 pubmed publisher..Our results suggest that PilN/O heterodimers form the foundation of the inner-membrane PilM/N/O/P complex, which is critical for the assembly of a functional T4P complex...
- Botuyan M, Mer G, Yi G, Koth C, Case D, Edwards A, et al. Solution structure and dynamics of yeast elongin C in complex with a von Hippel-Lindau peptide. J Mol Biol. 2001;312:177-86 pubmed..Moreover, the disappearance of conformational exchange phenomena on the microsecond to millisecond time scale within Elc1 upon VHL peptide binding suggests a role for slow internal motions in ligand recognition. ..
- Fabian M, White K. Analysis of a 3'-translation enhancer in a tombusvirus: a dynamic model for RNA-RNA interactions of mRNA termini. RNA. 2006;12:1304-14 pubmed..These results indicate that the 5'-3' RNA-RNA interaction is likely disrupted by scanning ribosomal subunits and suggest a dynamic model for the interaction of mRNA termini during active translation...
- Rakhit R, Chakrabartty A. Structure, folding, and misfolding of Cu,Zn superoxide dismutase in amyotrophic lateral sclerosis. Biochim Biophys Acta. 2006;1762:1025-37 pubmed..The relative merits of the two hypotheses are compared and a common unifying principle is outlined. Lastly, the potential for therapies targeting SOD1 misfolding is discussed. ..
- Wu N, Mo Y, Gao J, Pai E. Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. Proc Natl Acad Sci U S A. 2000;97:2017-22 pubmed publisher..The computational results are consistent with a catalytic mechanism that is characterized by Jencks's Circe effect...
- Mittermaier A, Kay L. Chi1 torsion angle dynamics in proteins from dipolar couplings. J Am Chem Soc. 2001;123:6892-903 pubmed..This study demonstrates that dipolar couplings may be used to characterize both the conformation of static residues and side-chain motion with high precision. ..
- Hiley S, Collins R. Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme. EMBO J. 2001;20:5461-9 pubmed
- Lee J, Cornell K, Riscoe M, Howell P. Structure of E. coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase reveals similarity to the purine nucleoside phosphorylases. Structure. 2001;9:941-53 pubmed..The structure of MTA/AdoHcy nucleosidase is the first structure of a prokaryotic nucleoside N-ribohydrolase specific for 6-aminopurines...
- Hayashi I, Ikura M. Crystal structure of the amino-terminal microtubule-binding domain of end-binding protein 1 (EB1). J Biol Chem. 2003;278:36430-4 pubmed..We propose that, like other actin-binding CH domains, EB1 employs the hydrophobic interaction to bind to microtubules. ..
- Tang X, Orlicky S, Lin Z, Willems A, Neculai D, Ceccarelli D, et al. Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination. Cell. 2007;129:1165-76 pubmed..This spatial variability may accommodate diverse acceptor lysine geometries in both substrates and the elongating ubiquitin chain and thereby increase catalytic efficiency. ..
- Mulligan V, Kerman A, Ho S, Chakrabartty A. Denaturational stress induces formation of zinc-deficient monomers of Cu,Zn superoxide dismutase: implications for pathogenesis in amyotrophic lateral sclerosis. J Mol Biol. 2008;383:424-36 pubmed publisher..Because the cytotoxicity of zinc-deficient SOD1 has been demonstrated previously, this species is a good candidate for the cytotoxic species in SOD1-associated amyotrophic lateral sclerosis. ..
- Stathopulos P, Zheng L, Li G, Plevin M, Ikura M. Structural and mechanistic insights into STIM1-mediated initiation of store-operated calcium entry. Cell. 2008;135:110-22 pubmed publisher..We provide atomic resolution insight into the molecular basis for STIM1-mediated SOCE initiation and show that the folded/unfolded state of the Ca2+-sensing region of STIM is crucial to SOCE regulation. ..
- Artz J, Dunford J, Arrowood M, Dong A, Chruszcz M, Kavanagh K, et al. Targeting a uniquely nonspecific prenyl synthase with bisphosphonates to combat cryptosporidiosis. Chem Biol. 2008;15:1296-306 pubmed publisher..These results, combined with existing data on their clinical use, demonstrate that N-BPs are very promising anticryptosporidial drug candidates...
- Zhao X, Yeung C, DONG V. Palladium-catalyzed ortho-arylation of O-phenylcarbamates with simple arenes and sodium persulfate. J Am Chem Soc. 2010;132:5837-44 pubmed publisher..We propose this oxidative arene cross-coupling occurs via two discrete C-H bond activations, namely cyclopalladation and electrophilic metalation, within a Pd(0/II) catalytic cycle...
- Ruschak A, Religa T, Breuer S, Witt S, Kay L. The proteasome antechamber maintains substrates in an unfolded state. Nature. 2010;467:868-71 pubmed publisher..We show that these substrates interact actively with the antechamber walls and have drastically altered kinetic and equilibrium properties that maintain them in unstructured states so as to be accessible for hydrolysis...
- Heon E, Priston M, Schorderet D, Billingsley G, Girard P, Lubsen N, et al. The gamma-crystallins and human cataracts: a puzzle made clearer. Am J Hum Genet. 1999;65:1261-7 pubmed..There is no direct evidence, to date, that up-regulation of a pseudogene causes cataracts. To our knowledge, these findings are the first evidence of an involvement of CRYGC and support the role of CRYGD in human cataract formation. ..
- Brown G, Singer A, Proudfoot M, Skarina T, Kim Y, Chang C, et al. Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis. Biochemistry. 2008;47:5724-35 pubmed publisher..coli...
- Baxter J, Moeder W, Urquhart W, Shahinas D, Chin K, Christendat D, et al. Identification of a functionally essential amino acid for Arabidopsis cyclic nucleotide gated ion channels using the chimeric AtCNGC11/12 gene. Plant J. 2008;56:457-69 pubmed publisher..This suggests that AtCNGC11/12 suppressors could be a useful tool for discovering important residues not only for plant CNGCs but also for CNGCs in general. ..
- Wybenga Groot L, Baskin B, Ong S, Tong J, Pawson T, Sicheri F. Structural basis for autoinhibition of the Ephb2 receptor tyrosine kinase by the unphosphorylated juxtamembrane region. Cell. 2001;106:745-57 pubmed..We propose that the autoinhibitory mechanism employed by EphB2 is a more general device through which receptor tyrosine kinases are controlled. ..
- Khorchid A, Inouye M, Ikura M. Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization. Biochem J. 2005;385:255-64 pubmed
- Lee J, Smith G, Horvatin C, Huang D, Cornell K, Riscoe M, et al. Structural snapshots of MTA/AdoHcy nucleosidase along the reaction coordinate provide insights into enzyme and nucleoside flexibility during catalysis. J Mol Biol. 2005;352:559-74 pubmed..A "catalytic movie" detailing substrate binding, catalysis, and product release is presented. ..
- Bello A, Poduch E, Fujihashi M, Amani M, Li Y, Crandall I, et al. A potent, covalent inhibitor of orotidine 5'-monophosphate decarboxylase with antimalarial activity. J Med Chem. 2007;50:915-21 pubmed publisher..2 +/- 0.7 microM against P. falciparum ItG and 3D7 isolates, respectively. 6-Iodouridine 5'-monophosphate is a novel covalent inhibitor of ODCase, and its nucleoside analogue paves the way to a new class of inhibitors against malaria...
- Tsai M, Koo J, Yip P, Colman R, Segall M, Howell P. Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism. J Mol Biol. 2007;370:541-54 pubmed..This loop movement has been observed in other superfamily enzymes, and has been proposed to be essential for catalysis. The ADL catalytic mechanism is re-examined in light of the results presented here. ..
- Mao D, Neculai D, Downey M, Orlicky S, Haffani Y, Ceccarelli D, et al. Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine. Mol Cell. 2008;32:259-75 pubmed publisher..Lastly, as Bud32 lacks the conventional substrate-recognition infrastructure of eukaryotic protein kinases including an activation segment, Bud32 may provide a glimpse of the evolutionary history of the protein kinase family...
- Hansen D, Zhou Z, Feng H, Miller Jenkins L, Bai Y, Kay L. Binding kinetics of histone chaperone Chz1 and variant histone H2A.Z-H2B by relaxation dispersion NMR spectroscopy. J Mol Biol. 2009;387:1-9 pubmed..Z-H2B to the chromatin remodeling complex, and the faster-than-diffusion association rate, 10(8) +/- 10(7) M(-1) s(-1), establishes the importance of attractive electrostatic interactions that form the chaperone-histone complex. ..
- Sampson P, Picard C, Handerson S, McGrath T, Domagala M, Leeson A, et al. Spiro-naphthyridinone piperidines as inhibitors of S. aureus and E. coli enoyl-ACP reductase (FabI). Bioorg Med Chem Lett. 2009;19:5355-8 pubmed publisher..Compounds 14a and 14c were identified as having sub-nanomolar E. coli FabI activity and are among the most potent FabI inhibitors yet described. The structural model of 14a bound to E. coli FabI is shown. ..
- Wu H, Min J, Lunin V, Antoshenko T, Dombrovski L, Zeng H, et al. Structural biology of human H3K9 methyltransferases. PLoS ONE. 2010;5:e8570 pubmed publisher..Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1. ..
- Bacik J, Walker J, Ali M, Schimmer A, Dhe Paganon S. Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme. J Biol Chem. 2010;285:20273-80 pubmed publisher..These studies reveal structural features that further our understanding of the UBA5 enzyme reaction mechanism and provide insight into the evolution of ubiquitin activation. ..
- Korzhnev D, Religa T, Banachewicz W, Fersht A, Kay L. A transient and low-populated protein-folding intermediate at atomic resolution. Science. 2010;329:1312-6 pubmed publisher..The approach introduces a general strategy for structure determination of low-populated and transiently formed protein states. ..
- Crowhurst K, Forman Kay J. Aromatic and methyl NOEs highlight hydrophobic clustering in the unfolded state of an SH3 domain. Biochemistry. 2003;42:8687-95 pubmed..Together, the results are also consistent with the folding funnel view involving multiple folding pathways for this molecule. ..
- Bezsonova I, Singer A, Choy W, Tollinger M, Forman Kay J. Structural comparison of the unstable drkN SH3 domain and a stable mutant. Biochemistry. 2005;44:15550-60 pubmed..Together these data provide evidence that both increasing the free energy of the folded state and decreasing the free energy of the unfolded state of the protein contribute to instability of the WT drkN SH3 domain. ..
- Stogios P, Chen L, Prive G. Crystal structure of the BTB domain from the LRF/ZBTB7 transcriptional regulator. Protein Sci. 2007;16:336-42 pubmed
- Payandeh J, Pai E. Enzyme-driven speciation: crystallizing Archaea via lipid capture. J Mol Evol. 2007;64:364-74 pubmed