Results 41 to 50 of about 6,634,608 (387)

Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis [PDF]

, 2015
Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening.
David Perahia, Divij Goyal, Gautier Moroy, Karen Druart, Maria A Miteva, Miteva MA, Olivier Sperandio, Saurabh Khemka, Shakti Rielland, Trott O, Xu X   +10 more
core   +4 more sources

CLP-based protein fragment assembly

, 2010
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a database of known
AGOSTINO DOVIER, ALESSANDRO DAL PALÙ, Dal Palù, Dotu, ENRICO PONTELLI, FEDERICO FOGOLARI, Levinthal   +6 more
core   +1 more source

Crystal structure of monomeric human β-2- microglobulin reveals clues to its amyloidogenic properties [PDF]

, 2002
Dissociation of human β-2-microglobulin (β(2)m) from the heavy chain of the class I HLA complex is a critical first step in the formation of amyloid fibrils from this protein.
A. P. Kalverda, Adams, Becker, Bellotti, Berman, Booth, C. H. Trinh, Collaborative Computational Project Number, Connors, D. P. Smith, Delaglio, Esposito, Floege, Hoshino, Kabsch, Kad, Khan, Khurana, Laskowski, Linke, McParland, Merritt, Morgan, Ohhashi, Okon, Richardson, S. E. Radford, S. E. V. Phillips, Saper, Smith, Verdone, Wang   +31 more
core   +2 more sources

Phosphorylation of huntingtin at residue T3 is decreased in Huntington’s disease and modulates mutant huntingtin protein conformation

Proceedings of the National Academy of Sciences of the United States of America, 2017
Significance The findings in this manuscript report on the identification of a posttranslational modification in the huntingtin protein (phosphorylation on residue T3 in the N17 region of the protein), which can revert the conformational effects of the ...
Cristina Cariulo, Lucia Azzollini, Margherita Verani, Paola Martufi, R. Boggio, Anass Chiki, Sean M. Deguire, Marta Cherubini, S. Ginés, J. L. Marsh, P. Conforti, E. Cattaneo, I. Santimone, F. Squitieri, Hilal A. Lashuel, Lara Petricca, A. Caricasole   +16 more
semanticscholar   +1 more source

Sequence-Dependent Correlated Segments in the Intrinsically Disordered Region of ChiZ

Biomolecules, 2020
How sequences of intrinsically disordered proteins (IDPs) code for their conformational dynamics is poorly understood. Here, we combined NMR spectroscopy, small-angle X-ray scattering (SAXS), and molecular dynamics (MD) simulations to characterize the ...
Alan Hicks, Cristian A. Escobar, Timothy A. Cross, Huan-Xiang Zhou   +3 more
doaj   +1 more source

Exploring the Levinthal limit in protein folding [PDF]

, 2017
According to the thermodynamic hypothesis, the native state of proteins is uniquely defined by their amino acid sequence. On the other hand, according to Levinthal, the native state is just a local minimum of the free energy and a given amino acid ...
B Fazi, B Hess, C Anfınsen, C Levinthal, C Orengo, D Baker, D Case, D van der Spoel, H Berman, H Gouda, J Sohl, JD Bryngelson, K Dill, L Cruzeiro, L Cruzeiro, L Cruzeiro, Leonor Cruzeiro, Léo Degrève, P Gettins, T Gallagher, T Lazaridis, TR Hynes, W Humphrey, W van Gunsteren   +23 more
core   +1 more source

The importance of RSV F protein conformation in VLPs in stimulation of neutralizing antibody titers in mice previously infected with RSV

Human Vaccines & Immunotherapeutics, 2017
Respiratory syncytial virus (RSV) is a significant respiratory pathogen but no vaccine is available. RSV infections present 2 major, unique problems. First, humans can experience repeated infections caused by the same virus sero-group indicating that ...
Lori M Cullen, M. Schmidt, T. Morrison
semanticscholar   +1 more source

Decoding F508del Misfolding in Cystic Fibrosis

Biomolecules, 2014
The functional deficiency of the cystic fibrosis transmembrane conductance regulator (CFTR), a plasma membrane chloride channel, leads to the development of cystic fibrosis.
Xiaodong Robert Wang, Chenglong Li
doaj   +1 more source

Reactive Human Plasma Glutathione Peroxidase Mutant with Diselenide Bond Succeeds in Tetramer Formation

Antioxidants, 2022
Plasma glutathione peroxidase (GPx3) belongs to the GPx superfamily, and it is the only known secreted selenocysteine (Sec)−containing GPx in humans.
Zhenlin Fan, Qi Yan, Jian Song, Jingyan Wei   +3 more
doaj   +1 more source

p97 Disease Mutations Modulate Nucleotide-Induced Conformation to Alter Protein-Protein Interactions. [PDF]

, 2016
The AAA+ ATPase p97/VCP adopts at least three conformations that depend on the binding of ADP and ATP and alter the orientation of the N-terminal protein-protein interaction (PPI) domain into up and down conformations.
Arkin, Michelle, Bulfer, Stacie, Chou, Tsui-Fen   +2 more
core