Results 101 to 110 of about 1,038,801 (318)

Refinement of homology-based protein structures by molecular dynamics simulation techniques

, 2004
The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated.
Mark, A. E., Fan, H., Mark, A E, Fan, H
core   +1 more source

Benchmark of Schemes for Multiscale Molecular Dynamics Simulations [PDF]

, 2015
In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and ...
Berendsen, Herman, Marrink, S. J.; id_orcid, de Vries, Alex; id_orcid, Goga, N., de Vries, Alex, Melo, M. N., Marrink, S. J., Hadar, A., Rzepiela, A. J.   +8 more
core   +1 more source

Epigenetic blind spots – the role of DNA methylation dynamics in stem cell‐based models of embryogenesis

FEBS Letters, EarlyView.
Embryo‐like structures (stembryos) are an innovative tool, but they are hindered by experimental variability and limited developmental potential. DNA methylation is crucial for mammalian development, but its status in stembryo models is poorly characterized.
Sara Canil, Anna Corrà, Annalisa Scapolatiello, Chengxiang Qiu, Gianluca Amadei   +4 more
wiley   +1 more source

Generative molecular dynamics

Current Opinion in Structural Biology
Understanding biomolecular function depends on bridging experimental observables with models that capture structural, stationary, and dynamical properties. Molecular dynamics (MD) simulations, in principle provide a bridge, but the sampling problem remains a fundamental roadblock toward this goal.
openaire   +2 more sources

pH‐mediated activation of the lysosomal arginine sensor SLC38A9

FEBS Letters, EarlyView.
Cells monitor nutrient levels via the lysosomal transporter SLC38A9 to activate the mechanistic target of rapamycin complex 1 (mTORC1). This study reveals that SLC38A9 function is regulated by pH. We identified histidine 544 as a critical pH sensor that undergoes conformational changes to control amino acid efflux from lysosomes; therefore, it ...
Xuelang Mu, Ampon Sae Her, Tamir Gonen
wiley   +1 more source

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

, 2006
Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release.
Fan, Hao, Mark, AE, Mark, Alan E., Alan E. Mark, Hao Fan, Fan, H   +5 more
core   +1 more source

Residual tail twisting in ascidian larvae is stabilized by asymmetric myofibrils that resist bilateral symmetry restoration

FEBS Letters, EarlyView.
Ascidian Ciona larvae initially show strong clockwise tail twisting, which is largely corrected during development. However, a small residual twist remains. This study shows that organized helical myofibrils in tail muscles mechanically stabilize this residual asymmetry, preventing complete restoration of bilateral symmetry and revealing how embryos ...
Yuki S. Kogure, Misaki K. Nishio, Satoru Okuda, Kohji Hotta   +3 more
wiley   +1 more source

High-resolution adaptive optical imaging within thick scattering media using closed-loop accumulation of single scattering

Nature Communications, 2017
Optical imaging deep in biological tissue is difficult due to multiple scattering and specimen induced aberrations of both the incident and reflected light. Here, Kang et al.
Sungsam Kang, Pilsung Kang, Seungwon Jeong, Yongwoo Kwon, Taeseok D. Yang, Jin Hee Hong, Moonseok Kim, Kyung–Deok Song, Jin Hyoung Park, Jun Ho Lee, Myoung Joon Kim, Ki Hean Kim, Wonshik Choi   +12 more
doaj   +1 more source

Ultraviolet photolysis of H2S and its implications for SH radical production in the interstellar medium

Nature Communications, 2020
Sulfur is abundant in the Universe, but the observed abundance ratio of SH to H2S doesn’t agree with astrochemical models. The authors measure product state-resolved translational energy spectra of photoproducts in a jet-cooled H2S beam as a function of ...
Jiami Zhou, Yarui Zhao, Christopher S. Hansen, Jiayue Yang, Yao Chang, Yong Yu, Gongkui Cheng, Zhichao Chen, Zhigang He, Shengrui Yu, Hongbin Ding, Weiqing Zhang, Guorong Wu, Dongxu Dai, Colin M. Western, Michael N. R. Ashfold, Kaijun Yuan, Xueming Yang   +17 more
doaj   +1 more source

Biophysical approaches for studying viral entry

FEBS Letters, EarlyView.
Viruses infect all living organisms and have been responsible for major epidemics and pandemics. Their ongoing evolutionary battle with host defenses creates a constant need for improved tools to study viral behavior. Advancing methods to probe viral attachment, fusion, and genome release deepen our understanding of how infections begin and support the
Inbar Yosibash, Raya Sorkin
wiley   +1 more source