Results 81 to 90 of about 1,038,801 (318)

Molecular dynamics simulations [PDF]

Current Biology, 1997
Originally the province of theorists only, molecular dynamics simulations are now accessible to a broad range of scientists. Advances in methodology, coupled with the development of fast and relatively inexpensive computer workstations, have increased the efficiency, accuracy, reliability, and applicability of these methods. Crossing important research
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

Machine-learning enhanced simulations predict graphene is microscopically hydrophobic and not wetting transparent

Nature Communications
The interaction between graphene and water is fundamental to applications ranging from filtration to nano-electronics, yet the intrinsic wettability of graphene remains a subject of longstanding debate.
Dianwei Hou, Yevhen Horbatenko, Stefan Ringe, Minhaeng Cho   +3 more
doaj   +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

Two-dimensional infrared spectroscopic study of cytochrome c peroxidase activity in deep eutectic solvent

Structural Dynamics, 2019
Deep eutectic solvents (DESs) prepared by mixing hydrogen-bond donor and acceptor molecules have been found to be of use in several applications. Recently, it was shown that DESs can enhance the peroxidation activity of cytochrome c.
Koji Osawa, Dorota Kossowska, Kwanghee Park, Kyungwon Kwak, Minhaeng Cho   +4 more
doaj   +1 more source

Infrared spectroscopic study of hydrogen bonding topologies in the smallest ice cube

Nature Communications, 2020
Spectroscopic studies of water clusters provide insight into the hydrogen bond structure of water and ice. The authors measure infrared spectra of neutral water octamers using a threshold photoionization technique based on a tunable vacuum-UV free ...
Gang Li, Yang-Yang Zhang, Qinming Li, Chong Wang, Yong Yu, Bingbing Zhang, Han-Shi Hu, Weiqing Zhang, Dongxu Dai, Guorong Wu, Dong H. Zhang, Jun Li, Xueming Yang, Ling Jiang   +13 more
doaj   +1 more source

Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2 [PDF]

, 2018
Phosphatidylinositol 4,5-bisphosphate (PIP2) acts as a signaling lipid, mediating membrane trafficking and recruitment of proteins to membranes. A key example is the PIP2-dependent regulation of the adhesion of L-selectin to the cytoskeleton adaptors of ...
Luo, Shi-Zhong, Marrink, Siewert J, Marrink, Siewert J; id_orcid, Carsten F.E. Schroer, Shi-Zhong Luo, Sun, Fude, Yin, Huiwei, Fude Sun, Xu, Lida, Lida Xu, Siewert J. Marrink, Schroer, Carsten F E, Huiwei Yin   +12 more
core   +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

Pseudoatom molecular dynamics

Physical Review E, 2015
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new method, which we call pseudoatom molecular dynamics (PAMD), can be applied to single or multi-component plasmas ...
Starrett, C. E., Daligault, J., Saumon, D.   +2 more
openaire   +4 more sources