Results 71 to 80 of about 6,540,405 (386)

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   +4 more sources

Evolutionary interplay between viruses and R‐loops

FEBS Letters, EarlyView.
Viruses interact with specialized nucleic acid structures called R‐loops to influence host transcription, epigenetic states, latency, and immune evasion. This Perspective examines the roles of R‐loops in viral replication, integration, and silencing, and how viruses co‐opt or avoid these structures.
Zsolt Karányi, Zita Képes, Zoltán Szabó, Eszter Csoma, Lóránt Székvölgyi   +4 more
wiley   +1 more source

Defining essential charged residues in fibril formation of a lysosomal derived N-terminal α-synuclein truncation

Nature Communications
N- and C-terminal α-synuclein (α-syn) truncations are prevalent in Parkinson’s disease. Effects of the N- and C-terminal residues on α-syn aggregation and fibril propagation are distinct, where the N-terminus dictates fibril structure. Here, the majority
Ryan P. McGlinchey, Sashary Ramos, Emilios K. Dimitriadis, C. Blake Wilson, Jennifer C. Lee   +4 more
doaj   +1 more source

Is protein folding problem really a NP-complete one ? First investigations

, 2013
To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D conformations, they ...
Bahi, Jacques M., Bienia, Wojciech, Côté, Nathalie, Guyeux, Christophe   +3 more
core   +3 more sources

Molecular modeling of an antigenic complex between a viral peptide and a class I major histocompatibility glycoprotein [PDF]

, 1992
Computer simulation of the conformations of short antigenic peptides (&lo residues) either free or bound to their receptor, the major histocompatibility complex (MHC)- encoded glycoprotein H-2 Ld, was employed to explain experimentally determined ...
Allen, Babbit, Bjorkman, Buus, Chen, Cramer, Del Val, DeLisi, Falk, Fauchère, Garrett, Jorgensen, Kidera, Kourilsky, Krug, Lambert, Lambert, Lambert, Margalit, Maryanski, Owen, Reddehase, Reddehase, Reddehase, Rötzschke, Saper, Schwartz, Serrano, Sette, Tirado-Rives, Townsend, Townsend, Townsend, Unanue, Van Bleek, Weiner, Wendoloski, Wold, Zinkernagel   +38 more
core   +1 more source

Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study

Scientific Reports, 2015
N-linked glycosylation is one of the most important, chemically complex and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes.
Hui-Sun Lee, Yifei Qi, W. Im
semanticscholar   +1 more source

Single‐cell insights into the role of T cells in B‐cell malignancies

FEBS Letters, EarlyView.
Single‐cell technologies have transformed our understanding of T cell–tumor cell interactions in B‐cell malignancies, revealing new T‐cell subsets, functional states, and immune evasion mechanisms. This Review synthesizes these findings, highlighting the roles of T cells in pathogenesis, progression, and therapy response, and underscoring their ...
Laura Llaó‐Cid
wiley   +1 more source

The role of C-terminal helix in the conformational transition of an arginine binding protein

Journal of Structural Biology: X, 2022
The thermotoga maritima arginine binding protein (TmArgBP) is a periplasmic binding protein that has a short helix at the C-terminal end (CTH), which is swapped between the two chains. We apply a coarse-grained structure-based model (SBM) and all-atom MD
Vinothini Santhakumar, Nahren Manuel Mascarenhas   +1 more
doaj   +1 more source

Biological and technical complexities in analyzing extracellular vesicle immune interactions in B‐cell malignancies

FEBS Letters, EarlyView.
Extracellular vesicles (EVs) mediate intercellular communication in tumor immune microenvironments. However, their role in B‐cell malignancies remains poorly defined, owing to biological complexity and technical challenges in EV isolation and analysis.
Daniel Bachurski, Michael Hallek
wiley   +1 more source

Understanding protein diffusion on force-induced stretched DNA conformation

Frontiers in Molecular Biosciences, 2022
DNA morphology is subjected to environmental conditions and is closely coupled with its function. For example, DNA experiences stretching forces during several biological processes, including transcription and genome transactions, that significantly ...
Anupam Mondal, Arnab Bhattacherjee
doaj   +1 more source