Results 91 to 100 of about 3,678,372 (337)

Conformational Dynamics of Phus [PDF]

Biophysical Journal, 2015
Iron is essential for pathogen's survival and virulence in the host and it requires specialized mechanisms for uptake and storage. PhuS is a cytoplasmic heme-trafficking protein in the opportunistic Gram-negative pathogen Pseudomonas aeruginosa. Heme binding to PhuS has been thought to occur by an induced-fit mechanism.
Yue, Zhi, Shen, Jana
openaire   +1 more source

Real‐time assay of ribonucleotide reductase activity with a fluorescent RNA aptamer

FEBS Letters, EarlyView.
Ribonucleotide reductases (RNR) synthesize DNA building blocks de novo, making them crucial in DNA replication and drug targeting. FLARE introduces the first single‐tube real‐time coupled RNR assay, which enables isothermal tracking of RNR activity at nanomolar enzyme levels and allows the reconstruction of allosteric regulatory patterns and rapid ...
Jacopo De Capitani, Noemi E. Nwosu, Viktoria Gocke, Müge Kasanmascheff, Hannes Mutschler   +4 more
wiley   +1 more source

Modelling conformational transitions in kinases by molecular dynamics simulations:achievements, difficulties and open challenges

Frontiers in Genetics, 2014
Protein kinases work because their flexibility allows to continuously switch from inactive to active form. Despite the large number of structures experimentally determined in such states, the mechanism of their conformational transitions as well as the ...
Marco eD'Abramo, Marco eD'Abramo, Neva eBesker, Giovanni eChillemi, Alessandro eGrottesi   +4 more
doaj   +1 more source

Substrate-induced conformational dynamics of the dopamine transporter

Nature Communications, 2019
The dopamine transporter is a member of the neurotransmitter:sodium symporters (NSSs), which are responsible for termination of neurotransmission through Na+-driven reuptake of neurotransmitter from the extracellular space.
A. Nielsen, Ingvar R. Möller, Yong Wang, S. Rasmussen, K. Lindorff‐Larsen, K. Rand, C. Loland   +6 more
semanticscholar   +1 more source

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review [PDF]

, 2011
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global ...
Daniel V. Veres, Eszter Hazai, Federico Miozzo, Francesco Piazza, Huba J. M. Kiss, Kuljeet Singh Sandhu, Peter Csermely, Ruth Nussinov, Zsolt Hoksza   +8 more
core   +4 more sources

Disordered but rhythmic—the role of intrinsic protein disorder in eukaryotic circadian timing

FEBS Letters, EarlyView.
Unstructured domains known as intrinsically disordered regions (IDRs) are present in nearly every part of the eukaryotic core circadian oscillator. IDRs enable many diverse inter‐ and intramolecular interactions that support clock function. IDR conformations are highly tunable by post‐translational modifications and environmental conditions, which ...
Emery T. Usher, Jacqueline F. Pelham
wiley   +1 more source

Conformational Dynamics and Cleavage Sites of Cas12a Are Modulated by Complementarity between crRNA and DNA

iScience, 2019
Summary Cas12a is an RNA-guided endonuclease, which displays great potentials and several advantages over the well-known Cas9 in genome editing and engineering. Here, we established a quantitative kinetic scheme to describe the conformational dynamics of
Lujia Zhang, Ruirui Sun, Mengyi Yang, Sijia Peng, Yongxin Cheng, Chunlai Chen   +5 more
semanticscholar   +1 more source

Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation

, 2014
In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field.
Apostolakis J., Astrakas L., Astrakas L. G., Bjelkmar P., Bohr H., Bohr H., Born B., Brooks C., Budi A., Budi A., Budi A., Christof Schütte, Ciccotti G., Ciccotti G., Ciccotti G., Damm M., Darden T., de la Hoz A., de Pomerai D., English N., Essmann U., Foloppe N., Gfeller D., Giovanni Ciccotti, Green M. S., Han Wang, Hess B., Inskip P. D., Jorgensen W. L., Kubo R., Luigi Delle Site, MacKerell A. D., Mancinelli F., Miyamoto S., Orlandini S., Orlandini S., Palla P., Parrinello M., Plusquellic D. F., Pronk S., Schütte C., Scovell D. L., Solomentsev G., Starzyk A., Toschi F., Vogel A.   +45 more
core   +1 more source

Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation

FEBS Letters, EarlyView.
Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe, Tanmay Kumar Mohanty, Rashna Bhandari, Dorothea Fiedler   +3 more
wiley   +1 more source

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

PLoS Computational Biology, 2009
Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states.
Barry J Grant, Alemayehu A Gorfe, J Andrew McCammon   +2 more
doaj   +1 more source