Results 111 to 120 of about 3,678,372 (337)

The newfound relationship between extrachromosomal DNAs and excised signal circles

FEBS Letters, EarlyView.
Extrachromosomal DNAs (ecDNAs) contribute to the progression of many human cancers. In addition, circular DNA by‐products of V(D)J recombination, excised signal circles (ESCs), have roles in cancer progression but have largely been overlooked. In this Review, we explore the roles of ecDNAs and ESCs in cancer development, and highlight why these ...
Dylan Casey, Zeqian Gao, Joan Boyes
wiley   +1 more source

Do Molecular Dynamics Force Fields Capture Conformational Dynamics of Alanine in Water?

Journal of Chemical Theory and Computation, 2019
We examine the ability of six molecular dynamics (MD) force fields (Amber ff14SB, Amber ff99SBnmr1, Amber ff03ws, OPLS-AA/L, OPLS-AA/M, and CHARMM36) to reproduce conformational ensembles of the central alanine in GAG and AAA in a way that is consistent ...
Shuting Zhang, R. Schweitzer‐Stenner, B. Urbanc   +2 more
semanticscholar   +1 more source

Inherent flexibility and protein function: the open/closed conformational transition of the N-terminal domain of calmodulin

, 2008
The key to understanding a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility and function of N-terminal ...
Portman, John J., Tripathi, Swarnendu
core   +1 more source

RosettaBackrub--a web server for flexible backbone protein structure modeling and design. [PDF]

, 2010
The RosettaBackrub server (http://kortemmelab.ucsf.edu/backrub) implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling.
Friedland, Gregory F, Humphris, Elisabeth L, Kortemme, Tanja, Lauck, Florian, Smith, Colin A   +4 more
core   +2 more sources

Conserved structural motifs in PAS, LOV, and CRY proteins regulate circadian rhythms and are therapeutic targets

FEBS Letters, EarlyView.
Cryptochrome and PAS/LOV proteins play intricate roles in circadian clocks where they act as both sensors and mediators of protein–protein interactions. Their ubiquitous presence in signaling networks has positioned them as targets for small‐molecule therapeutics. This review provides a structural introduction to these protein families.
Eric D. Brinckman, Anna E. Lester, Brian D. Zoltowski   +2 more
wiley   +1 more source

Origin of conformational dynamics in a globular protein

Communications Biology, 2019
Protein structures are dynamic, undergoing motions that can play a vital role in function. However, the link between primary sequence and conformational dynamics remains poorly understood.
A. Damry, M. M. Mayer, A. Broom, Natalie K. Goto, R. Chica   +4 more
semanticscholar   +1 more source

Molecular Simulations of the Ribosome and Associated Translation Factors

, 2014
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information.
Hamed H. Alsulami (532535), Muhammad Bilal Ashraf (532534), Muhammad Shahab Alhuthali (532536), Tasawar Hayat (433317)   +3 more
core   +6 more sources

In situ molecular organization and heterogeneity of the Legionella Dot/Icm T4SS

FEBS Letters, EarlyView.
We present a nearly complete in situ model of the Legionella Dot/Icm type IV secretion system, revealing its central secretion channel and identifying new components. Using cryo‐electron tomography with AI‐based modeling, our work highlights the structure, variability, and mechanism of this complex nanomachine, advancing understanding of bacterial ...
Przemysław Dutka, Yuxi Liu, Stefano Maggi, Debnath Ghosal, Jue Wang, Prashant P. Damke, Stephen D. Carter, Wei Zhao, Sukhithasri Vijayrajratnam, Joseph P. Vogel, Carrie L. Shaffer, Grant J. Jensen   +11 more
wiley   +1 more source

Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies

Biomolecules
Pulsed electron–electron double resonance (PELDOR) spectroscopy is a powerful method for determining nucleic acid (NA) structure and conformational dynamics.
Alexey S. Chubarov, Burkhard Endeward, Maria A. Kanarskaya, Yuliya F. Polienko, Thomas F. Prisner, Alexander A. Lomzov   +5 more
doaj   +1 more source

The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET

Cell Reports, 2018
Summary: Off-target binding and cleavage by Cas9 pose major challenges in its application. How the conformational dynamics of Cas9 govern its nuclease activity under on- and off-target conditions remains largely unknown.
Mengyi Yang, Sijia Peng, Ruirui Sun, Jingdi Lin, Nan Wang, Chunlai Chen   +5 more
doaj   +1 more source