Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations

Autor: H.A.M. Pepermans, R.C. van Schaik, Andrea Amadei, L.D Creveld, H.J.C. Berendsen, J. de Vlieg

Publikováno v: Proteins-Structure Function and Genetics, 33(2), 253-264. Wiley

The implementation of cutinase from Fusarium solani pisi as a fat-stain removing ingredient in laundry washing is hampered by its unfolding in the presence of anionic surfactants. In this work we present molecular dynamics (MD) computer simulations o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c1dc10a571325235975a4ac72fe60a07
https://doi.org/10.1002/(sici)1097-0134(19981101)33:2<253::aid-prot9>3.0.co

Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme

Autor: Steven Hayward, H.J.C. Berendsen

Publikováno v: Proteins: Structure, Function, and Genetics. 30:144-154

Methods developed originally to analyze domain motions from simulation (Proteins 27:425-437, 1997) are adapted and extended for the analysis of X-ray conformers and for proteins with more than two domains. The method can be applied as an automatic pr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a6d3d36ce4d48670a18ab89cabc8fcb0
https://doi.org/10.1002/(sici)1097-0134(19980201)30:2<144::aid-prot4>3.0.co

On the use of the quasi-Gaussian entropy theory in noncanonical ensembles. I. Prediction of temperature dependence of thermodynamic properties

Autor: M. E. F. Apol, H.J.C. Berendsen, Andrea Amadei

Publikováno v: Journal of Chemical Physics, 109(8), 3004-3016. AMER INST PHYSICS

In previous articles we derived and tested the quasi-Gaussian entropy theory, a description of the excess Helmholtz free energy in terms of the potential energy distribution, instead of the configurational partition function. We obtained in this way

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dc4c4a393cec27ed115d77c52108f7e9
https://doi.org/10.1063/1.476893

An Efficient, Box Shape Independent Non-Bonded Force and Virial Algorithm for Molecular Dynamics

Autor: M.K.R. Renardus, H.J.C. Berendsen, E.J Dijkstra, H. Bekker

Publikováno v: Molecular Simulation, 14(3), 13-32

A notation is introduced and used to transform a conventional specification of the non-bonded force and virial algorithm in the case of periodic boundary conditions into an alternative specification. The implementation of the transformed specificatio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0d350fc6470b7c0e3fc70e089c2a19e
https://doi.org/10.1080/08927029508022012

A structural determinant of the behavior of water at hydration and nanoconfinement conditions.

Autor: Loubet NA; INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina., Verde AR; INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina., Appignanesi GA; INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina. appignan@criba.edu.ar.

Publikováno v: The European physical journal. E, Soft matter [Eur Phys J E Soft Matter] 2024 Sep 30; Vol. 47 (9), pp. 61. Date of Electronic Publication: 2024 Sep 30.