Studying protein interactions, dynamics and complexes
Single-molecule studies of the dynamics and interactions of bacterial OXPHOS complexes
... and dynamics of bioenergetic complexes in two dimensions in the plane of the membrane is not well understood and has implications for the operation of the system as a ...and dynamics can be ...
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Assessment of ab initio models of protein complexes by molecular dynamics
... of protein complexes by molecular dynamics Radom, Filip ; Plückthun, Andreas ; Paci, Emanuele Abstract: Determining how proteins interact to form stable complexes is of crucial importance, for ...
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Assessment of ab initio models of protein complexes by molecular dynamics.
... stable complexes is of crucial importance, for example in the development of novel ...of complexes from the structure of the binding part- ners, such as RosettaDock, might potentially emerge to become a ...
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A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes
... Step 1: Use short runs of Molecular Dynamics to generate an ensemble of protein complex conformations... Introduction Related Work Methods Results Conclusion.[r] ...
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Free energy calculations of protein-ligand complexes with computational molecular dynamics
... Since the Lennard-Jones potential decays with r −6 , additional forces can be neglected for larger r. However, the use of such a cut-off for the Coulomb potential is known to cause severe artifacts 64,62, 65 due to its ...
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A study of biomolecular interactions using three biological complexes to explore structure, dynamics and method development
... determine how well a molecule can permeate cells [133], however for the purpose of this experiment, Vega calculations are used to determine the heat capacity of the complex as a crys[r] ...
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A new computational approach to analyze human protein complexes and predict novel protein interactions
... Discovery of new interactors of PAK1 by combining PEGO with 'wet' biological experiments The potential of PEGO has been confirmed by 'wet' biological experiments testing the in silico results obtained by submit- ting ...
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Dynamics of ligand-protein interactions - impact on drug discovery
... We also wanted to attempt to answer the question - how many simulations are needed to provide a “good coverage” of the conformational space (75% or greater)?. Here the results of the two largest eigenvector movements ...
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Computationally modeling interactions and dynamics to promote the understanding of protein function
... Introduction In a simplistic view, life can be described as a hierarchical organization of complex biological structures and systems [Solomon et al., 2002, pages 9-10]: In the lowest level are atoms that covalently bind ...
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Intermolecular interactions and protein dynamics by solid state NMR spectroscopy
... backbone dynamics spanning over nine orders of magnitude in time scale for the protein GB1 in two different environments: a crystalline form and the precipitated GB1:IgG complex with a molecular weight of ...
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Predicting and characterising protein-protein complexes
... et al., 2005; Grunberg et al., 2004; Krol et al., 2007a). A similar approach is that of Mustard and Ritchie (2005), in which the program CONCOORD (de Groot et al., 1997) was used to generate an ensemble of structures ...
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Optimization of Electrostatic Interactions in Protein-Protein Complexes
... decoy complexes delivered with rigid body approach, the structures of the monomers are the same among the decoys and WT and the only difference is the binding ...decoy complexes is the electrostatic ...
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Modeling protein interactions in protein binding sites and oligomeric protein complexes
... Furthermore, incorporating both side-chain and backbone flexibility in docking methods still represents a major problem, because it greatly increases the compu- tational time required both during the sampling space, as ...
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Evolution of protein complexes by duplication of homomeric interactions
... multi- protein complex, but many alternative ones, which may not co-exist in time and in ...within protein complexes. For example, a protein complex composed of six identical subunits forming ...
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Dynamics and thermodynamics of protein-ligand interactions
... both cis and trans isomers, and with the double bond placed at different positions. Entropically, previously predicted penalties for rotamerically ‘freezing’ a single ligand C- C bond upon binding, used for important ...
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Spatial chemical conservation of hot spot interactions in protein-protein complexes
... aromatic interactions) are created by the conserved YY motif (Tyr-54, Tyr-55, 1bxi numbering) ...conserved interactions are the hydrogen bonds formed by Glu-30 and Asp-51 and a hydrophobic aliphatic ...
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Hypoxia inducible factor (HIF) as a model for studying inhibition of protein–protein interactions
... p300 interaction interface by focusing on one of the two key helices. 120 An ITC binding experiment between the CH1 domain of p300 and C-TAD HIF-1a 799 Ac-TAADCEYNAR 804 which corre- sponds to the helix 2 region; ...
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Studying Protein-Protein Interactions via Blot Overlay or Far Western Blot
... many protein-protein interactions rely upon aspects of secondary and tertiary protein structure that are disrupted under reducing and denaturing conditions, it might seem likely that few if ...
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Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions
... on protein-protein in- terfaces, specifically of interfaces involved in transient ...make interactions only with the interactor (inter-) and those that make in- teractions with the interactor and ...
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Hydrogen Exchange Mass Spectrometry for Studying Protein- Ligand Interactions
... Our HDX data reveal that the interaction of ADEP1 with ClpP causes both local changes and allosteric switching. Ligand binding in the apical region induces a major rigidification of the equatorial region. This ...
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