Genomes and Genes
Experts and Doctors on molecular models in Rockville, Maryland, United States
Locale: Rockville, Maryland, United States
Topic: molecular models
- Zawadzke L, Smith T, Herzberg O. An engineered Staphylococcus aureus PC1 beta-lactamase that hydrolyses third-generation cephalosporins. Protein Eng. 1995;8:1275-85 pubmed..aureus beta-lactamase structure, widening the active site cleft and providing space to accommodate the bulky side-chains of the third-generation cephalosporins. ..
- Chen C, Smith T, Kapadia G, Wäsch S, Zawadzke L, Coulson A, et al. Structure and kinetics of the beta-lactamase mutants S70A and K73H from Staphylococcus aureus PC1. Biochemistry. 1996;35:12251-8 pubmed..A crystal soaked with ampicillin was flash-frozen, and diffraction data were collected at 2.1 A resolution. The electron density map showed no indication of substrate binding. ..
- Bera A, Atanasova V, Gamage S, Robinson H, Parsons J. Structure of the D-alanylgriseoluteic acid biosynthetic protein EhpF, an atypical member of the ANL superfamily of adenylating enzymes. Acta Crystallogr D Biol Crystallogr. 2010;66:664-72 pubmed publisher..Based on the structure of EhpF and a bioinformatic analysis, it is proposed that EhpF and EhpG convert phenazine-1,6-dicarboxylate to 6-formylphenazine-1-carboxylate via an adenylyl intermediate. ..
- Chen C, Herzberg O. Inhibition of beta-lactamase by clavulanate. Trapped intermediates in cryocrystallographic studies. J Mol Biol. 1992;224:1103-13 pubmed..The salt bridge enhances the stability of the cis product, while the steric strain introduced by the short contacts with the protein reduces its stability. ..
- Lin D, Tanaka Y, Iwasaki M, Gittis A, Su H, Mikami B, et al. The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors. Proc Natl Acad Sci U S A. 2008;105:3011-6 pubmed publisher..The immune receptor-like loops offer a new surface for further study and potentially the design of molecules that would affect PD-1/PD-L1 complex formation and thereby modulate the immune response. ..
- Radaev S, Kattah M, Rostro B, Colonna M, Sun P. Crystal structure of the human myeloid cell activating receptor TREM-1. Structure. 2003;11:1527-35 pubmed..As a result, the dimeric TREM-1 most likely contains two distinct ligand binding sites. ..
- Cho S, Wang Q, Swaminathan C, Hesek D, Lee M, Boons G, et al. Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins. Proc Natl Acad Sci U S A. 2007;104:8761-6 pubmed
- Dimasi N, Sawicki M, Reineck L, Li Y, Natarajan K, Margulies D, et al. Crystal structure of the Ly49I natural killer cell receptor reveals variability in dimerization mode within the Ly49 family. J Mol Biol. 2002;320:573-85 pubmed..Such variability may enable certain Ly49 receptors, like Ly49I, to bind MHC-I molecules bivalently, thereby stabilizing receptor-ligand interactions and enhancing signal transmission to the NK cell. ..
- McCutchan T, Piper R, Makler M. Use of malaria rapid diagnostic test to identify Plasmodium knowlesi infection. Emerg Infect Dis. 2008;14:1750-2 pubmed publisher..We report the use of a rapid test to supplement microscopic analysis in distinguishing the 5 malaria species that infect humans...
- Cho S, Velikovsky C, Swaminathan C, Houtman J, Samelson L, Mariuzza R. Structural basis for differential recognition of tyrosine-phosphorylated sites in the linker for activation of T cells (LAT) by the adaptor Gads. EMBO J. 2004;23:1441-51 pubmed
- Sundberg E, Li H, Llera A, McCormick J, Tormo J, Schlievert P, et al. Structures of two streptococcal superantigens bound to TCR beta chains reveal diversity in the architecture of T cell signaling complexes. Structure. 2002;10:687-99 pubmed..Thus, highly efficient T cell activation may be achieved through structurally diverse strategies of TCR ligation...
- Kasiviswanathan R, Shin J, Melamud E, Kelman Z. Biochemical characterization of the Methanothermobacter thermautotrophicus minichromosome maintenance (MCM) helicase N-terminal domains. J Biol Chem. 2004;279:28358-66 pubmed..It is also shown that although oligomerization is not essential for single-stranded DNA binding and ATPase activity, the presence of domain C is essential for helicase activity...
- Teplyakov A, Obmolova G, Sarikaya E, Pullalarevu S, Krajewski W, Galkin A, et al. Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism. J Bacteriol. 2004;186:7134-40 pubmed
- Li Y, Li H, Dimasi N, McCormick J, Martin R, Schuck P, et al. Crystal structure of a superantigen bound to the high-affinity, zinc-dependent site on MHC class II. Immunity. 2001;14:93-104 pubmed..Thus, SPE-C may optimize T cell responses by mimicking the peptide dependence of conventional antigen presentation and recognition...
- Herzberg O, Reddy P, Sutrina S, Saier M, Reizer J, Kapadia G. Structure of the histidine-containing phosphocarrier protein HPr from Bacillus subtilis at 2.0-A resolution. Proc Natl Acad Sci U S A. 1992;89:2499-503 pubmed
- Teplyakov A, Lim K, Zhu P, Kapadia G, Chen C, Schwartz J, et al. Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein. Proc Natl Acad Sci U S A. 2006;103:16218-23 pubmed
- Radaev S, Rostro B, Brooks A, Colonna M, Sun P. Conformational plasticity revealed by the cocrystal structure of NKG2D and its class I MHC-like ligand ULBP3. Immunity. 2001;15:1039-49 pubmed..Unlike the KIR receptors that recognize a conserved HLA region by a lock-and-key mechanism, NKG2D recognizes diverse ligands by an induced-fit mechanism. ..
- Zhang H, Huang K, Li Z, Banerjei L, Fisher K, Grishin N, et al. Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications. Proteins. 2000;40:86-97 pubmed publisher..By analogy, YbaK may also play a role in nucleotide or oligonucleotide binding, the nature of which is yet to be determined...
- Charneski L, Patel P, Sym D. Telavancin: a novel lipoglycopeptide antibiotic. Ann Pharmacother. 2009;43:928-38 pubmed publisher..To review the pharmacology, antimicrobial activity, pharmacokinetics, clinical applications, and safety of telavancin, a new lipoglycopeptide antibiotic...
- Ames J, Ikura M. Structure and membrane-targeting mechanism of retinal Ca2+-binding proteins, recoverin and GCAP-2. Adv Exp Med Biol. 2002;514:333-48 pubmed..The Ca2+-induced structural changes in these proteins are important for elucidating their membrane-targeting mechanisms and for understanding the molecular mechanism of Ca2+-sensitive regulation of phototransduction. ..
- Sundberg E, Sawicki M, Southwood S, Andersen P, Sette A, Mariuzza R. Minor structural changes in a mutated human melanoma antigen correspond to dramatically enhanced stimulation of a CD4+ tumor-infiltrating lymphocyte line. J Mol Biol. 2002;319:449-61 pubmed..Defining the structural basis by which CD4+ T cell help is invoked in an anti-tumor immune response will likely aid the design of more effective cancer immunotherapies. ..
- Boyington J, Sun P. A structural perspective on MHC class I recognition by killer cell immunoglobulin-like receptors. Mol Immunol. 2002;38:1007-21 pubmed..Furthermore, unexpected similarities with T-cell receptor (TCR) recognition of MHC molecules are also observed. The detailed interactions between KIR and HLA-C molecules and their functional implications will be reviewed here. ..
- Li Y, Huang Y, Lue J, Quandt J, Martin R, Mariuzza R. Structure of a human autoimmune TCR bound to a myelin basic protein self-peptide and a multiple sclerosis-associated MHC class II molecule. EMBO J. 2005;24:2968-79 pubmed
- Zhuravleva M, Trandem K, Sun P. Structural implications of Siglec-5-mediated sialoglycan recognition. J Mol Biol. 2008;375:437-47 pubmed
- Goll J, Rajagopala S, Shiau S, Wu H, Lamb B, Uetz P. MPIDB: the microbial protein interaction database. Bioinformatics. 2008;24:1743-4 pubmed publisher..In contrast to these databases, interactions in MPIDB are further supported by 8150 additional evidences based on interaction conservation, co-purification and 3D domain contacts (iPfam, 3did). http://www.jcvi.org/mpidb/ ..
- He Y, Chen Y, Alexander P, Bryan P, Orban J. NMR structures of two designed proteins with high sequence identity but different fold and function. Proc Natl Acad Sci U S A. 2008;105:14412-7 pubmed publisher..This result has implications for understanding not only the folding code but also the evolution of new folds. ..
- Li Y, Cao C, Jia W, Yu L, Mo M, Wang Q, et al. Structure of the F-spondin domain of mindin, an integrin ligand and pattern recognition molecule. EMBO J. 2009;28:286-97 pubmed publisher..Through these dual interactions, the FS and TSR domains of mindin promote activation of both adaptive and innate immune responses. ..
- Smith N, Roitberg A, Rivera E, Howard A, Holden M, Mayhew M, et al. Structural analysis of ligand binding and catalysis in chorismate lyase. Arch Biochem Biophys. 2006;445:72-80 pubmed..The two sites are connected by a short tunnel that is partly open at each end, suggesting that CL may operate via a 2-site or tunnel mechanism. ..
- Han M, Hannick L, DiBrino M, Robinson M. Polymorphism of human CD1 genes. Tissue Antigens. 1999;54:122-7 pubmed..The substitution in CD1e is located in the region predicted to interact with ligands and may differentially impact the ability of CD1e alleles to bind antigen. ..
- Yeh D, Parsons L, Parsons J, Liu F, Eisenstein E, Orban J. NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog. Protein Sci. 2005;14:424-30 pubmed publisher..Despite this level of sequence homology, significant differences exist between the two structures. These differences are described along with possible functional implications of the structures...
- Herzberg O. An atomic model for protein-protein phosphoryl group transfer. J Biol Chem. 1992;267:24819-23 pubmed..The second, during the transfer, is intermolecular, with 2 aspartate residues associated with the active site of IIA(Glc). Such alternating ion pairs may be mechanistically important in other protein-protein phosphotransfer reactions. ..
- Ladner J, Obmolova G, Teplyakov A, Howard A, Khil P, Camerini Otero R, et al. Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site. BMC Struct Biol. 2003;3:7 pubmed publisher..The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme...
- Lim K, Zhang H, Tempczyk A, Krajewski W, Bonander N, Toedt J, et al. Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot. Proteins. 2003;51:56-67 pubmed publisher..The substrate-binding domain is absent in HI0766 sequence family and may be provided by another Haemophilus influenzae partner protein, which is yet to be identified...
- Ridge K. Algal rhodopsins: phototaxis receptors found at last. Curr Biol. 2002;12:R588-90 pubmed..Sequence and architecture comparisons among this growing family highlight key components for light-responsive functions. ..
- Sawicki M, Dimasi N, Natarajan K, Wang J, Margulies D, Mariuzza R. Structural basis of MHC class I recognition by natural killer cell receptors. Immunol Rev. 2001;181:52-65 pubmed..The complex structures provide a framework for understanding MHC-I recognition by NK receptors from both families and reveal striking differences in the nature of this recognition, despite the receptors' functional similarity. ..
- Varela P, Llera A, Mariuzza R, Tormo J. Crystal structure of imaginal disc growth factor-2. A member of a new family of growth-promoting glycoproteins from Drosophila melanogaster. J Biol Chem. 2002;277:13229-36 pubmed..Thus, IDGFs may have evolved from chitinases to acquire new functions as growth factors, interacting with cell surface glycoproteins implicated in growth-promoting processes, such as the Drosophila insulin receptor. ..
- Ladner J, Reddy P, Davis A, Tordova M, Howard A, Gilliland G. The 1.30 A resolution structure of the Bacillus subtilis chorismate mutase catalytic homotrimer. Acta Crystallogr D Biol Crystallogr. 2000;56:673-83 pubmed..In this structure, the C-terminal tails of the subunits of the trimer are hydrogen bonded to residues of the active site of neighboring trimers in the crystal and thus cross-link the molecules in the crystal lattice. ..
- Su H, Golden J, Gittis A, Hooper J, Garboczi D. Structural basis for the binding of the neutralizing antibody, 7D11, to the poxvirus L1 protein. Virology. 2007;368:331-41 pubmed..In addition, the sequence and structure of Fab-7D11 will contribute to the development of L1-targeted immunotherapeutics...
- Boyington J, Gladyshev V, Khangulov S, Stadtman T, Sun P. Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. Science. 1997;275:1305-8 pubmed..These structures suggest a reaction mechanism that directly involves SeCys140 and His141 in proton abstraction and the molybdenum, molybdopterin, Lys44, and the Fe4S4 cluster in electron transfer. ..
- Lagüe P, Roux B, Pastor R. Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids. J Mol Biol. 2005;354:1129-41 pubmed..An extension of the classical surfactant theory of Israelachvili based on shapes is proposed to introduce the concept of a "dynamically induced shape" of the membrane lipids by the peptide. ..
- Mans B, Ribeiro J. A novel clade of cysteinyl leukotriene scavengers in soft ticks. Insect Biochem Mol Biol. 2008;38:862-70 pubmed publisher..As such, modulation of the hemostatic system as well as inflammation was important adaptive responses in the evolution of a blood-feeding lifestyle in soft ticks...
- Tormo J, Natarajan K, Margulies D, Mariuzza R. Crystal structure of a lectin-like natural killer cell receptor bound to its MHC class I ligand. Nature. 1999;402:623-31 pubmed..Both Ly49A binding sites on MHC-I are spatially distinct from that of the T-cell receptor. ..
- Killian B, Kravitz J, Somani S, Dasgupta P, Pang Y, Gilson M. Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide. J Mol Biol. 2009;389:315-35 pubmed publisher..The results also reveal intricate structure-entropy relationships. Thus, the present analysis suggests that in order for a model of binding to be accurate, it must include a careful accounting of configurational entropy changes. ..
- Boesen C, Radaev S, Motyka S, Patamawenu A, Sun P. The 1.1 A crystal structure of human TGF-beta type II receptor ligand binding domain. Structure. 2002;10:913-9 pubmed..The first finger in the TBRII is significantly longer than in ActRII and BRIA and folds tightly between the second finger and the C terminus. Surface charge distributions and hydrophobic patches predict potential TBRII binding sites. ..
- Pieper U, Kapadia G, Zhu P, Peterkofsky A, Herzberg O. Structural evidence for the evolutionary divergence of mycoplasma from gram-positive bacteria: the histidine-containing phosphocarrier protein. Structure. 1995;3:781-90 pubmed..As there is no evidence of a conformational change accompanying Ser46 phosphorylation, the inhibitory effect of this event may be attributable to altered surface electrostatics. ..
- Teplyakov A, Pullalarevu S, Obmolova G, Doseeva V, Galkin A, Herzberg O, et al. Crystal structure of the YffB protein from Pseudomonas aeruginosa suggests a glutathione-dependent thiol reductase function. BMC Struct Biol. 2004;4:5 pubmed..Given the conservation of the functionally important residues and the ability to bind glutathione, YffB is likely to function as a GSH-dependent thiol reductase. ..
- Tangrea M, Bryan P, Sari N, Orban J. Solution structure of the pro-hormone convertase 1 pro-domain from Mus musculus. J Mol Biol. 2002;320:801-12 pubmed..The PC1 pro-domain structure also reveals potential mechanisms for the acid-induced dissociation of the complex between pro- and catalytic domains. ..
- Radaev S, Zou Z, Tolar P, Nguyen K, Nguyen A, Krueger P, et al. Structural and functional studies of Igalphabeta and its assembly with the B cell antigen receptor. Structure. 2010;18:934-43 pubmed publisher..These studies provide the first structural model for understanding BCR function. ..
- Syin C, Parzy D, Traincard F, Boccaccio I, Joshi M, Lin D, et al. The H89 cAMP-dependent protein kinase inhibitor blocks Plasmodium falciparum development in infected erythrocytes. Eur J Biochem. 2001;268:4842-9 pubmed..Finally, structural considerations suggest that drugs targeting the parasite, rather than the erythrocyte enzyme, might be developed that could help in the fight against malaria. ..
- Sun P, Radaev S, Kattah M. Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases. Acta Crystallogr D Biol Crystallogr. 2002;58:1092-8 pubmed
- Garman S, Garboczi D. The molecular defect leading to Fabry disease: structure of human alpha-galactosidase. J Mol Biol. 2004;337:319-35 pubmed..The structure of human alpha-GAL brings Fabry disease into the realm of molecular diseases, where insights into the structural basis of the disease phenotypes might help guide the clinical treatment of patients. ..
- Su H, Garman S, Allison T, Fogg C, Moss B, Garboczi D. The 1.51-Angstrom structure of the poxvirus L1 protein, a target of potent neutralizing antibodies. Proc Natl Acad Sci U S A. 2005;102:4240-5 pubmed..The structure of L1 is a step in the elucidation of molecular mechanisms common to all poxviruses that may stimulate the design of safer vaccines and new antipoxvirus drugs. ..
- Guan R, Wang Q, Sundberg E, Mariuzza R. Crystal structure of human peptidoglycan recognition protein S (PGRP-S) at 1.70 A resolution. J Mol Biol. 2005;347:683-91 pubmed..Differences in PGN-contacting residues and interactions suggest that, although PGRPs may engage PGNs in a similar mode, structural differences exist that likely regulate the affinity and fine specificity of PGN recognition. ..