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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Zhou, Wen Xia, Tian Tong, Jiansong Dickerson, Julie Su, Bo Gu, Xun Department of Mathematics Iowa State University Ames IA 50010 United States Program of Bioinformatics and Computational Biology Iowa State University Ames IA 50010 United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA 50010 United States Department of Genetics Development and Cell Biology Iowa State University Ames IA 50010 United States

ISBN: (纸本)1424415098

Exocytosis is an essential process in all eukaryotic cells that allows communication in cells through vesicles which contain a wide range of intracellular molecules such as hormones, matrix proteins and neurotransmitters. Recent studies have shown this process is regulated by molecular interactions among a group of well defined and conserved proteins. To gain insight into the dynamics of these interactions, we use protein interaction network modeling to investigate exocytotic system (particularly in endocrine) computationally and mathematically. The protein interactions are formulated into ordinary differential equations (ODE). We then apply a novel mathematic approach to estimate model parameters from experimental data for SNAREs-only network (with three key proteins), which is a subset of this system. Our approach is able to sense temporal changes in protein concentration and ratios of multiple proteins and precisely reconstruct the dynamical process of exocytosis, including vesicle docking, priming and fusion. Additionally, the model suggests that initial concentration of synaptic proteins plays a crucial role in efficiency of vesicle fusion, based on system stability analysis. ©2007 IEEE.

关键词： Proteins

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PRTAD: A database for protein residue torsion angle distributions

PRTAD: A database for protein residue torsion angle distribu...

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IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

作者： Xiaoyong Sun Di Wu Robert Jernigan Zhijun Wu Program on Bioinformatics and Computational Biology Department of Mathematics Western Kentucky University Bowling Green KY USA Department of Biochemistry Biophysics and Molecular Biology Department of Mathematics Iowa State University Ames IA USA

PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level "virtual" bond and torsion angles obtained from their distributions in databases of known protein structures such as in the PDB Data Bank. PRTAD is capable of generating, caching, and displaying the statistical distributions of the angles of various types. The collected information can be used to extract geometric restraints or define statistical potentials for protein structure determination. PRTAD is supported with a friendly designed web interface so that users can easily specify the angle types, and retrieve, visualize, or download the distributions of the angles as they desire. The database PRTAD is freely accessible at http://***/prtad.

关键词： Bonding Spatial databases Protein engineering Amino acids Bioinformatics computational biology Mathematics Data mining Niobium compounds Nuclear magnetic resonance

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EXPERIMENTAL AND THEORETICAL STUDIES OF HYDROGEN BONDS IN FE-S PROTEINS

EXPERIMENTAL AND THEORETICAL STUDIES OF HYDROGEN BONDS IN FE...

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第十二届北京分析测试学术报告会暨展览会(BCEIA 2007)

作者： William M.WESTLER I-Jin LIN Erika B.GEBEL Timothy E.MACHONKIN Bin XIA John L.MARKLEY National Magnetic Resonance Facility at Madison University of Wisconsin-Madison Department of Biochemistry University of Wisconsin-Madison Graduate Program in Biophysics University of Wisconsin-Madison Program in Molecular and Computational Biophysics Johns Hopkins University Department of Chemical Biology College of Life Sciences Peking University

Iron-sulfur proteins are ubiquitous and essential to *** addition to their functional roles as electron transport proteins in photosynthesis and respiration,iron-sulfur proteins also are involved in nitrogen fixation,... 详细信息

关键词： NMR EXPERIMENTAL AND THEORETICAL STUDIES OF HYDROGEN BONDS IN FE-S PROTEINS

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Comparison of experimental and computed protein anisotropic temperature factors

Comparison of experimental and computed protein anisotropic ...

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IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

作者： Lei Yang Guang Song Robert L. Jernigan Program of Bioinformatics and Computational Biology Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA USA Department of Computer Science Iowa State University Ames IA USA Department of Biochemistry Biophysics and Molecular Biology L. H. Baker Center for Bioinformatics and Biological Statistics Iowa State University Ames IA USA

Because of its appealing simplicity, the anisotropic network model (ANM) has been widely accepted and applied to study many molecular motion problems: such as the molecular mechanisms of GroEL-GroES function, allosteric changes in hemoglobin, ribosome motion, motor-protein motions, and conformational changes in general, etc. However, the validity of the ANM has not been closely examined. In this work, we use ANM to predict the anisotropic temperature factors of proteins. On the flip side, the rich, directional anisotropic temperature factor data available for hundreds of proteins in the protein data bank (PDB) are used as validation data to closely test the ANM model. The significance of this work is that it presents a timely, important evaluation of the model, shows the extent of its accuracy in reproducing experimental anisotropic temperature factors, and suggests ways to improve the model. An improved model will help us better understand the internal dynamics of proteins, which in turn can greatly expand the usefulness of the models, which has already been demonstrated in many applications.

关键词： Proteins Anisotropic magnetoresistance Temperature Fluctuations computational biology biology computing Computer networks Bioinformatics Biochemistry biophysics

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Proteins hunt and gatherAssociated Content

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Nature 2007年第7147期447卷 920-921页

作者： David Eliezer Arthur G. Palmer David Eliezer is in the Department of Biochemistry and the Program in Structural Biology Weill Cornell Medical College New York New York 10021 USA. dae2005@med.cornell.edu Arthur G. Palmer III is in the Department of Biochemistry and Molecular Biophysics Columbia University New York New York 10032 USA. agp6@columbia.edu

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Identifying interaction sites in "Recalcitrant" proteins: Predicted protein and RNA binding sites in REV proteins of HIV-1 and EIAV agree with experimental data

Identifying interaction sites in "Recalcitrant" proteins: Pr...

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11th Pacific Symposium on Biocomputing 2006, PSB 2006

作者： Terribllini, Michael Lee, Jae-Hyung Yan, Changhui Jernigan, Robert L. Carpenter, Susan Honavar, Vasant Dobbs, Drena Bioinformatics and Computational Biology Graduate Program LH. Baker Center for Bioinformatics and Biological Statistics Iowa State University Ames IA 50010 United States Department of Computer Science Iowa State University Ames IA 50010 United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA 50010 United States Department of Genetics Development and Cell Biology Iowa State University Ames IA 50010 United States Artificial Intelligence Research Laboratory Center for Computational Intelligence Learning and Discovery Iowa State University Ames IA 50010 United States Department of Veterinary Microbiology and Pathology Washington State University Pullman WA. 99164 United States

ISBN: (纸本)9812564632

Protein-protein and protein nucleic acid interactions are vitally important for a wide range of biological processes, including regulation or gene expression, protein synthesis, and replication and assembly of many viruses. We have developed machine learning approaches for predicting which amino acids of a protein participate in its interactions with other proteins and/or nucleic acids, using only the proiein sequence as input. In this paper, we describe an application of classifiers trained on datasets of well-characterized protein-protein and protein-RNA complexes for which experimental structures are available. We apply these classifiers to the problem of predicting protein and RNA binding sites in the sequence of a clinically important protein for which the structure is not known: the regulatory protein Rev, essential for the replication of HIV-I and other lentiviruses. We compare our predictions with published biochemical, genetic and partial structural information for HIV-1 and EIAV Rev and with our own published experimental mapping of RNA binding sites in EIAV Rev. The predicted and experimentally determined binding sites are in very good agreement. The ability to predict reliably the residues of a protein that directly contribute to specific binding events - without the requirement for structural information regarding either the protein or complexes in which it participates - can potentially generate new disease intervention strategies.

关键词： Binding sites

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Refinement of NMR-determined protein structures with database derived distance constraints

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Journal of Bioinformatics and computational biology 2005年第6期3卷 1315-1329页

作者： Cui, Feng Jernigan, Robert Wu, Zhijun Program on Bioinformatics and Computational Biology Iowa State University Ames IA 50011 United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA 50011 United States Department of Mathematics Program on Bioinformatics and Computational Biology Iowa State University Ames IA 50011 United States

The protein structures determined by NMR (Nuclear Magnetic Resonance Spectroscopy) are not as detailed and accurate as those by X-ray crystallography and are often underdetermined due to the inadequate distance data available from NMR experiments. The uses of NMR-determined structures in such important applications as homology modeling and rational drug design have thus been severely limited. Here we show that with the increasing numbers of high quality protein structures being determined, a computational approach to enhancing the accuracy of the NMR-determined structures becomes possible by deriving additional distance constraints from the distributions of the distances in databases of known protein structures. We show through a survey on 462 NMR structures that, in fact, many inter-atomic distances in these structures deviate considerably from their database distributions and based on the refinement results on 10 selected NMR structures that these structures can actually be improved significantly when a selected set of distances are constrained within their high probability ranges in their database distributions. © Imperial College Press.

关键词： NMR protein structure refinement Protein structure database structural bioinformatics

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NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure

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Journal of structural and Functional Genomics 2005年第1期6卷 51-62页

作者： Hervé Du Penhoat, Catherine Li, Zhaohui Atreya, Hanudatta S. Kim, Seho Yee, Adelinda Xiao, Rong Murray, Diana Arrowsmith, Cheryl H. Szyperski, Thomas Department of Chemistry University of Buffalo State University of New York Buffalo NY 14260 United States Department of Microbiology and Immunology Institute for Computational Biomedicine B-314 Weill Medical College of Cornell University New York NY 10021 1300 York Avenue United States Division of Molecular and Structural Biology Ontario Cancer Institute Toronto Ont. Canada Department of Medical Biophysics University of Toronto Toronto Ont. Canada Center for Advanced Biotechnology and Medicine Department of Molecular Biology and Biochemistry Rutgers University Piscataway NJ 08854 679 Hoes Lane United States Northeast Structural Genomics Consortium Rutgers University Piscataway NJ 08854 610 Taylor Road United States Chemistry Department Rutgers University Piscataway NJ 08854 610 Taylor Road United States

The 150-residue protein TM1509 is encoded in gene YF09_THEMA of Thermotoga maritima. TM1509 has so far no functional annotation and belongs to protein family UPF0054 (PFAM accession number: PF02130) which contains at least 146 members. The NMR structure of TM1509 reveals an α+β fold comprising a four stranded β-sheet with topology A(↑), B(↑), D(↑), C(↓) as well as five α-helices I-V. The structures of most members of family PF02130 can be reliably constructed using the TM1509 NMR structure, demonstrating high leverage for exploration of fold space. A multiple sequence alignment of TM1509 with homologues of family UPF0054 shows that three polypeptide segments, as well as a putative zinc-binding consensus motif HGXLHLXGYDH located at the C-terminal end of α-helix IV, are highly conserved. The spatial arrangement of the three His residues of this UPF0054 consensus motif is similar to the arrangement found for the His residues in the HEXXHXXGXXH zinc-binding consensus motif of matrix metallo-proteases (MMPs). Moreover, the other conserved polypeptide segments form a large cavity which encloses the putative Zn-binding pocket and might confer specificity during catalysis. However, TM1509 and the other members of the UPF0054 family do not have the crucial Glu residue in position 2 of the MMP consensus motif. Intriguingly, the TM1509 structure indicates that the Asp in the UPF0054 consensus motif (Asp 111 in TM1509) may overtake the catalytic role of the Glu. This suggests that protein family UPF0054 might contain members of a hitherto uncharacterized class of metalloproteases. © Springer 2005.

关键词： Matrix metalloproteinase structural genomics Thermotoga maritima TM1509 UPF0054 Zinc-binding protein

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Biochemistry: Rev1 employs a novel mechanism of DNA synthesis using a protein template

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Science 2005年第5744期309卷 2219-2222页

作者： Nair, Deepak T. Johnson, Robert E. Prakash, Louise Prakash, Satya Aggarwal, Aneel K. Structural Biology Program Department of Physiology and Biophysics Mount Sinai School of Medicine 1425 Madison Avenue New York NY 10029 United States Sealy Center for Molecular Science University of Texas Medical Branch 6.014 Medical Research Building 11th and Mechanic Streets Galveston TX 77755-1061 United States

The Rev1 DNA polymerase is highly specialized for the incorporation of C opposite template G. We present here the crystal structure of yeast Rev1 bound to template G and incoming 2′-deoxycytidine 5′-triphosphate (dCTP), which reveals that the polymerase itself dictates the identity of the incoming nucleotide, as well as the identity of the templating base. Template G and incoming dCTP do not pair with each other. Instead, the template G is evicted from the DNA helix, and it makes optimal hydrogen bonds with a segment of Rev1. Also, unlike other DNA polymerases, incoming dCTP pairs with an arginine rather than the templating base, which ensures the incorporation of dCTP over other incoming nucleotides. This mechanism provides an elegant means for promoting proficient and error-free synthesis through N2-adducted guanines that obstruct replication.

关键词： DNA

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The 3-Dimensional Architecture of Platelets in the Native State by Electron Cryotomography.

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Blood 2005年第11期106卷 1658-1658页

作者： Michael P. Marsh Juan Chang Junmei Chen Jose Lopez Wah Chiu Structural and Computational Biology and Molecular Biophysics and Vera and Marrs McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston TX USA Thrombosis Research Section Department of Medicine Baylor College of Medicine Houston TX USA

Conventional electron microscopy requires that samples be chemically fixed, embedded in plastic and stained prior to examination. This technique always raises uncertainty as to whether the observations are faithful to the native cellular organization. These limitations are overcome with the technique of electron cryomicroscopy, in which samples are prepared and observed in the frozen, hydrated state. A modification of this technique, electron cryotomography, is a method capable of recording images from the same specimen area at different tilt angles under low electron dose conditions, revealing the spatial relationships of organelles and molecular assemblies within a cell that has not been subjected to chemical fixation or metal staining. Here, we used electron cryotomography to examine the 3-dimensional architecture of platelets in the resting state and in various stages of activation. Platelets in citrated plasma isolated from healthy human subjects were allowed to settle onto a perforated carbon grid and frozen immediately in liquid ethane or were allowed to settle for different time periods on a grid coated with fibrillar type 1 collagen before being frozen. The platelets suspended across holes were embedded in a thin layer of vitreous ice. Successive images of these frozen, hydrated platelets were then acquired as the stage was tilted through a range of ±70° using a JEM2010F electron cryomicroscope. Each image was recorded using a 4kx4k CCD camera. The digital images were computationally aligned and merged to reconstruct a 3-dimensional density map with an 4.0 gigapixel volume. Multiple tilt-series were reconstructed and analyzed using segmentation and visualization tools. The platelet reconstructions were annotated in terms of the sizes, shapes and relative locations of the subcellular components, including mitochondria, α and dense granules, dense clusters, the dense tubular system, microtubules, and the surface-connected canalicular system. We observed great

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