Results 51 to 60 of about 707,163 (239)

A model of protein conformational substates [PDF]

Proceedings of the National Academy of Sciences, 1985
Many proteins have been observed to exist in a large number of conformations that are believed to play an important role in their dynamics. A model of protein conformational substates that incorporates the ideas of frustration and disorder in analogy to glasses and spin glasses is proposed.
openaire   +2 more sources

Protein Allostery and Conformational Dynamics [PDF]

Chemical Reviews, 2016
The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding
Jingjing, Guo, Huan-Xiang, Zhou
openaire   +2 more sources

Calpain small subunit homodimerization is robust and calcium‐independent

FEBS Letters, EarlyView.
Calpains dimerize via penta‐EF‐hand (PEF) domains. Using single‐molecule force spectroscopy, we measured the strength and kinetics of PEF–PEF homodimer binding. The interaction is robust, shows a transient conformational step before dissociation, and remains largely insensitive to Ca2+.
Nesha May O. Andoy, Trina Dykstra‐MacPherson, Mathias A. Bell, Peter L. Davies, Ruby May A. Sullan   +4 more
wiley   +1 more source

Structural insights into an engineered feruloyl esterase with improved MHET degrading properties

FEBS Letters, EarlyView.
A feruloyl esterase was engineered to mimic key features of MHETase, enhancing the degradation of PET oligomers. Structural and computational analysis reveal how a point mutation stabilizes the active site and reshapes the binding cleft, expading substrate scope.
Panagiota Karampa, Konstantinos Makryniotis, Theofani‐Iosifina Sousani, Evangelos Topakas, Vangelis Daskalakis, Maria Dimarogona   +5 more
wiley   +1 more source

Quantitative Protein Dynamics from Dominant Folding Pathways

, 2007
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding problem are ...
F. Pederiva, G. Garberoglio, H. Orland, M. Sega, M. M. Klosek, P. Faccioli, van Gunsteren   +6 more
core   +1 more source

Gut microbiome and aging—A dynamic interplay of microbes, metabolites, and the immune system

FEBS Letters, EarlyView.
Age‐dependent shifts in microbial communities engender shifts in microbial metabolite profiles. These in turn drive shifts in barrier surface permeability of the gut and brain and induce immune activation. When paired with preexisting age‐related chronic inflammation this increases the risk of neuroinflammation and neurodegenerative diseases.
Aaron Mehl, Eran Blacher
wiley   +1 more source

A methionine‐lined active site governs carbocation stabilization and product specificity in a bacterial terpene synthase

FEBS Letters, EarlyView.
This study reveals a unique active site enriched in methionine residues and demonstrates that these residues play a critical role by stabilizing carbocation intermediates through novel sulfur–cation interactions. Structure‐guided mutagenesis further revealed variants with significantly altered product profiles, enhancing pseudopterosin formation. These
Marion Ringel, Carl P. O. Helmer, Shani Zev, Ronja Driller, Emily Buhr, Markus Reinbold, Renana Schwartz, Gabriel Foley, Mikael Boden, Daniel Garbe, Gerhard Schenk, Dan Thomas Major, Bernhard Loll, Thomas Brück   +13 more
wiley   +1 more source

Valosin‐containing protein counteracts ATP‐driven dissolution of FUS condensates through its ATPase activity in vitro

FEBS Letters, EarlyView.
Biomolecular condensates formed by fused in sarcoma (FUS) are dissolved by high ATP concentrations yet persist in cells. Using a reconstituted system, we demonstrate that valosin‐containing protein (VCP), an AAA+ ATPase, counteracts ATP‐driven dissolution of FUS condensates through its D2 ATPase activity.
Hitomi Kimura, Shin‐ichi Tate, Kyota Yasuda   +2 more
wiley   +1 more source

Primary Sequences of Protein-Like Copolymers: Levy Flight Type Long Range Correlations

, 2001
We consider the statistical properties of primary sequences of two-letter HP copolymers (H for hydrophobic and P for polar) designed to have water soluble globular conformations with H monomers shielded from water inside the shell of P monomers. We show,
A. Irbäck, A. Irbäck, A.R. Khokhlov, A.R. Khokhlov, Alexander L. Borovinsky, Alexander Yu. Grosberg, Alexei R. Khokhlov, E.A. Zheligovskaya, Elena N. Govorun, I. Grosse, J. Virtanen, N.V. Dokholyan, Pavel G. Khalatur, V. Pande, V.A. Ivanov, V.I. Lozinskii, V.S. Pande, Victor A. Ivanov   +17 more
core   +1 more source

Conformational Dynamics Simulations of Proteins [PDF]

, 1999
Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds.
Eichinger, Markus, Heymann, Berthold, Heller, Helmut, Grubmüller, Helmut, Tavan, Paul, Hermans, J., Deuflhard, P., Mark, A. E., Leimkuhler, B., Reich, S., Skeel, R. D.   +10 more
openaire   +2 more sources