Coupled Residue-Residue Dynamics in Protein Allosteric Mechanisms
نویسندگان
چکیده
منابع مشابه
Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation.
Detailed understanding of how conformational dynamics orchestrates function in allosteric regulation of recognition and catalysis remains ambiguous. Here, we simulate CypA using multiple-microsecond-long atomistic molecular dynamics in explicit solvent and carry out NMR experiments. We analyze a large amount of time-dependent multidimensional data with a coarse-grained approach and map key dyna...
متن کاملProtein-protein docking with multiple residue conformations and residue substitutions.
The protein docking problem has two major aspects: sampling conformations and orientations, and scoring them for fit. To investigate the extent to which the protein docking problem may be attributed to the sampling of ligand side-chain conformations, multiple conformations of multiple residues were calculated for the uncomplexed (unbound) structures of protein ligands. These ligand conformation...
متن کاملResidue-residue mean-force potentials for protein structure recognition.
We present two new sets of energy functions for protein structure recognition, given the primary sequence of amino acids along the polypeptide chain. The first set of potentials is based on the positions of alpha- and the second on positions of beta- and alpha-carbon atoms of amino acid residues. The potentials are derived using a theory of Boltzmann-like statistics of protein structure. The en...
متن کاملUniversality in protein residue networks.
Residue networks representing 595 nonhomologous proteins are studied. These networks exhibit universal topological characteristics as they belong to the topological class of modular networks formed by several highly interconnected clusters separated by topological cavities. There are some networks that tend to deviate from this universality. These networks represent small-size proteins having <...
متن کاملPredicting protein residue-residue contacts using deep networks and boosting
MOTIVATION Protein residue-residue contacts continue to play a larger and larger role in protein tertiary structure modeling and evaluation. Yet, while the importance of contact information increases, the performance of sequence-based contact predictors has improved slowly. New approaches and methods are needed to spur further development and progress in the field. RESULTS Here we present DNC...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2017
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2016.11.2490