نتایج جستجو برای: conformations analysis

تعداد نتایج: 2835289  

Journal: :Protein science : a publication of the Protein Society 2005
Chu Wang Ora Schueler-Furman David Baker

Success in high-resolution protein-protein docking requires accurate modeling of side-chain conformations at the interface. Most current methods either leave side chains fixed in the conformations observed in the unbound protein structures or allow the side chains to sample a set of discrete rotamer conformations. Here we describe a rapid and efficient method for sampling off-rotamer side-chain...

2013
Justin Ritz Joshua S. Martin Alain Laederach

Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs. For certain RNAs (e.g. riboswitches), a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. If alternative secondary structures are important to the function of an RNA, we expect to observe evolutionary co-variation supporting multiple conformations. W...

Journal: :Journal of chemical information and modeling 2010
Simone Fulle Nina Alexandra Christ Eva Kestner Holger Gohlke

We report all-atom molecular dynamics and replica exchange molecular dynamics simulations on the unbound human immunodeficiency virus type-1 (HIV-1) transactivation responsive region (TAR) RNA structure and three TAR RNA structures in bound conformations of, in total, approximately 250 ns length. We compare the extent of observed conformational sampling with that of the conceptually simpler and...

Journal: :Acta crystallographica. Section D, Structural biology 2016
Trung Thanh Thach Donghyuk Shin Seungsu Han Sangho Lee

The conformational flexibility of linkage-specific polyubiquitin chains enables ubiquitylated proteins and their receptors to be involved in a variety of cellular processes. Linear or Met1-linked polyubiquitin chains, associated with nondegradational cellular signalling pathways, have been known to adopt multiple conformations from compact to extended conformations. However, the extent of such ...

Journal: :Journal of molecular biology 1987
C Chothia A M Lesk

We have analysed the atomic structures of Fab and VL fragments of immunoglobulins to determine the relationship between their amino acid sequences and the three-dimensional structures of their antigen binding sites. We identify the relatively few residues that, through their packing, hydrogen bonding or the ability to assume unusual phi, psi or omega conformations, are primarily responsible for...

2005
BJÖRN GRUNDBERG

The purpose of this project was to enhance and interpret electron microscopy images of the Sodium Potassium ATPase, that is a cell membrane protein, and to develop a computer application that made all the needed steps in the analysis. The hypothesis that should be examined was that there was more than one possible conformation of protein unit cells in the crystal images of the ATPase, but it wa...

Journal: :The journal of physical chemistry. B 2009
Andrew L Ferguson Pablo G Debenedetti Athanassios Z Panagiotopoulos

We employ molecular dynamics simulations to study the solubility and molecular conformations of n-alkane chains in water. We find nearly exponential decrease in solubility with carbon number up to n-eicosane (C(20)), and excellent agreement with experiment up to n-dodecane (C(12)). We detect no sharp break in the dependence of the solubility upon carbon number. A free energy landscape analysis ...

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2015
Matthew Merski Marcus Fischer Trent E Balius Oliv Eidam Brian K Shoichet

Conformational change in protein-ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few substantial series of congeneric ligand complexes in the Protein Data Bank (PDB). Here we determine the structures of eight alkyl benzenes, in single-m...

Journal: :Biochemistry 2011
Young-Tae Lee Edith C Glazer Richard F Wilson C David Stout David B Goodin

Conformational changes in the substrate access channel have been observed for several forms of cytochrome P450, but the extent of conformational plasticity exhibited by a given isozyme has not been completely characterized. Here we present crystal structures of P450cam bound to a library of 12 active site probes containing a substrate analogue tethered to a variable linker. The structures provi...

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2011
Adelene Y L Sim Michael Levitt

RNA often folds hierarchically, so that its sequence defines its secondary structure (helical base-paired regions connected by single-stranded junctions), which subsequently defines its tertiary fold. To preserve base-pairing and chain connectivity, the three-dimensional conformations that RNA can explore are strongly confined compared to when secondary structure constraints are not enforced. U...

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