Results 11 to 20 of about 1,442,239 (292)

Glassy Dynamics of Protein Folding [PDF]

Physical Review E, 1999
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis dynamics at low ...
Ayşe Erzan, B. Erman, B. Erman, B. Ewen, D. ben-Avraham, Erkan Tüzel, H. Frauenfelder, J. Colmenero, J. L. Green, K. A. Dill, M. Levitt, M. M. Tirion, N. Go, P. G. Wolynes, P. J. Flory, R. Mélin, T. Haliloǧlu, W. Feller   +17 more
core   +5 more sources

Functional Dynamics of Proteins [PDF]

Computational and Mathematical Methods in Medicine, 2012
X-ray crystallography captures protein conformational states that are stable enough to be captured. These observable states are simply part of the functional event in the context of protein dynamics. Life at the molecular level has a vibrant nature at physiological temperature, governed by physics laws. Molecular dynamics (MDs) simulations have been
Lee-Wei Yang, Silvina Matysiak, Shang-Te Danny Hsu, Gabriela Mustata Wilson, Joti Yasumasa   +4 more
openaire   +2 more sources

Dynamic Proteins in Bacteria [PDF]

Developmental Cell, 2001
The MinCDE system regulates the position of the division plane in rod-shaped bacteria. New results from Escherichia coli provide insight into how this operates by showing that MinE stimulates the ATPase activity of MinD.
Autret S, Errington J
openaire   +3 more sources

Functional protein dynamics in a crystal. [PDF]

Nat Commun, 2023
Abstract Proteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales.
Klyshko E, Kim JS, McGough L, Valeeva V, Lee E, Ranganathan R, Rauscher S.   +6 more
europepmc   +6 more sources

Protein dynamics

FEBS Letters, 1994
Modern NMR has revitalized the study of protein dynamics. Multidimensional spectra and the heteronuclear spectroscopy allow a substantial gain in resolution. Dynamics can be analyzed at individual sites and data on segmental and sequence‐dependent flexibility are accumulating.
Jardetzky, Oleg, Lefèvre, Jean-François   +1 more
openaire   +2 more sources

A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations

Frontiers in Molecular Biosciences, 2022
Protein-protein interactions are at the basis of many protein functions, and the knowledge of 3D structures of protein-protein complexes provides structural, mechanical and dynamical pieces of information essential to understand these functions. Protein-protein interfaces can be seen as stable, organized regions where residues from different partners ...
Martin, Juliette, Frezza, Elisa
openaire   +3 more sources

Sec translocon has an insertase-like function in addition to polypeptide conduction through the channel [version 1; peer review: 4 approved]

F1000Research, 2019
The Sec translocon provides a polypeptide-conducting channel, which is insulated from the hydrophobic lipidic environment of the membrane, for translocation of hydrophilic passenger polypeptides.
Koreaki Ito, Naomi Shimokawa-Chiba, Shinobu Chiba   +2 more
doaj   +1 more source

Water Dynamics at Protein Interfaces: Ultrafast Optical Kerr Effect Study [PDF]

, 2012
The behavior of water molecules surrounding a protein can have an important bearing on its structure and function. Consequently, a great deal of attention has been focused on changes in the relaxation dynamics of water when it is located at the protein ...
Bizzarri A. R., Bizzarri A. R., Born B., Bucaro J. A., Castner E. W., Chang Y. J., Colaianni S. E. M., de Morais L. C., Eaves J. D., Ebbinghaus S., Eriksson K. O., Feig M., Giraud G., Halle B., Halle B., Hamm P., Heisler I. A., Heisler I. A., Heugen U., Heyden M., Hunt N. T., Hunt N. T., Hunt N. T., Hunt N. T., Ismael A. Heisler, James T. L., Kamila Mazur, Kato A., Kuntz I. D., Laage D., Laage D., Lang E. W., Lee B., Lee B., Lerbret A., Levy Y., Lotshaw W. T., Mahn A., Malardier-Jugroot C., Marchi M., Marti J., Mazur K., Mazur K., Mazzacurati V., McMorrow D., Mizoguchi K., Modig K., Moon Y. U., Murphy W. F., Nakayama T., Nandi N., Nielsen O. F., Ohmine I., Ohmine I., Paolantoni M., Perticaroli S., Potma E. O., Qvist J., Qvist J., Rejoumichel A., Rezus Y. L. A., Rupley J. A., Russo D., Shenogina N., Shirota H., Shirota H., Smith N. A., Stephen R. Meech, Stirnemann G., Torre R., Urabe H., Winkler K., Xu J., Yokoyama K., Zhong Q.   +74 more
core   +1 more source

A Dynamical Approach to Protein Folding [PDF]

Journal of Biological Physics, 2001
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the native configuration.
A. TORCINI, LIVI, ROBERTO, A. POLITI
openaire   +4 more sources

Lasso-grafting of macrocyclic peptide pharmacophores yields multi-functional proteins

Nature Communications, 2021
RaPID (Random non-standard Peptides Integrated Discovery) enables discovery of small macrocyclic peptides binding desired targets. Here, the authors propose lasso-grafting: the RaPID-derived peptides are implanted onto diverse proteins and maintain both ...
Emiko Mihara, Satoshi Watanabe, Nasir K. Bashiruddin, Nozomi Nakamura, Kyoko Matoba, Yumi Sano, Rumit Maini, Yizhen Yin, Katsuya Sakai, Takao Arimori, Kunio Matsumoto, Hiroaki Suga, Junichi Takagi   +12 more
doaj   +1 more source