Benjamin Stamm, How to make continuum solvation incredibly fast in a few simple steps: a practical guide to the domain decomposition paradigm for the Conductor-like Screening Model Continuum Solvation, Linear Scaling, Domain Decomposition, , 2019 pp. 1-25.
(pdf)
David A C Beck et al., A microscopic view of peptide and protein solvation, Biophysical Chemistry, 100 (2002) 221-237.
(web, pdf)
Andreas Krämer et al., Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects, Journal Of Chemical Theory And Computation, 15 (2019) 3854-3867.
(web, pdf)
Stephen J Perkins, Protein volumes and hydration effects, European Journal Of Biochemistry, 157 (1986) 169-180.
Amino acid sequences, carbohydrate compositions and residue volumes are used to compare critically calculations of partial specific volumes v̄, neutron scattering matchpoints and 280‐nm absorption co...
(web, pdf)
Marco Pezzella et al., Water Dynamics Around Proteins: T- and R-States of Hemoglobin and Melittin, Arxiv.Org, 2020 32589026, physics.chem-ph p. acs.jpcb.0c04320.
The water dynamics, as characterized by the local hydrophobicity (LH), is investigated for tetrameric hemoglobin and dimeric melittin. For the T0 to R0 transition in Hb it is found that LH provides additional molecular-level insight into the Perutz mechanism, i.e., the breaking and formation of salt bridges at the alpha1 / beta2 and alpha2 / beta1 interface is accompanied by changes in LH. For Hb in cubic water boxes with 90 Aengstroem and 120 Aengstroem edge length it is observed that following a decrease in LH as a consequence of reduced water density or change of water orientation at the protein/water interface the alpha / beta interfaces are destabilized; this is a hallmark of the Perutz stereochemical model for the T to R transition in Hb. The present work thus provides a dynamical view of the classical structural model relevant to the molecular foundations of Hb function. For dimeric melittin, earlier results by Cheng and Rossky (Nature, 1998, 392, 696-699) are confirmed and interpreted on the basis of LH from simulations in which the protein structure is frozen. For the flexible melittin dimer the changes in the local hydration can be as much as 30 % than for the rigid dimer, reflecting the fact that protein and water dynamics are coupled.
(web, pdf)