A microscopic view of protein solvation

Lounnas, Valère; Pettitt, B. Montgomery; Findsen, Leonore A.; Subramaniam, Shankar

doi:10.1021/j100197a004

Cited by 35 publications

(23 citation statements)

References 3 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A number of recent molecular dynamics (MD) studies of model mesoscopic solutes: colloid particles, graphene sheets, protein molecules, etc., were aimed at quantification of the intermolecular interaction potentials on the length scales of a water molecule [40][41][42][43][44][49][50][51][52][53][54][55][56][57]. As expected, these studies demonstrate in these potentials a primary attractive minimum, mostly due to the van der Waals interactions.…”

Section: Molecular Processes Underlying the Thermodynamics Of Proteinmentioning

confidence: 75%

Nucleation and Growth Mechanisms of Protein Crystals

Vekilov

2015

Handbook of Crystal Growth

View full text Add to dashboard Cite

Section: Molecular Processes Underlying the Thermodynamics Of Proteinmentioning

confidence: 75%

Nucleation and Growth Mechanisms of Protein Crystals

Vekilov

2015

Handbook of Crystal Growth

View full text Add to dashboard Cite

“…The properties of water molecules appear distinct from bulk water when in proximity to proteins. Experiments and theoretical studies1–6 have provided considerable evidence that the properties of water, such as diffusion constant, residence time, dipole moment, and hydrogen bond dynamics, etc., are different when around a protein than those of bulk water. Generally, the diffusion rates of water molecules within 4–5 Å of a protein surface have been found to be significantly different from that in bulk water.…”

Section: Introductionmentioning

confidence: 99%

Effects of dimerization of Serratia marcescens endonuclease on water dynamics

et al. 2006

Self Cite

View full text Add to dashboard Cite

The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

show abstract

“…Site‐directed mutagenesis also has been used to probe the importance of internal water molecules to protein stability, where site mutants have been designed to either displace known ordered water molecules or to create a cavity within the protein structure 9–11. Finally, molecular dynamics simulations, in the absence of experimental data, have probed the water structure around proteins 12–21…”

Section: Introductionmentioning

confidence: 99%

Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study

Schiffer

Gunsteren

1999

Proteins

View full text Add to dashboard Cite

Water plays an essential role in most biological processes. Water molecules solvating biomolecules are generally in fast exchange with the environment. Nevertheless, well-defined electron density is seen for water associated with proteins whose crystal structure is determined to high resolution. The relative accessibility of these water sites is likely to be relevant to their biological role but is difficult to assess. A time-averaging crystallographic refinement simulation on basic pancreatic trypsin inhibitor successfully characterizes the relative accessibility of the crystallographic water sites. In such a refinement simulation water diffuses through the crystal lattice in a manner that is consistent with the crystallographic data. This refinement discovers that internal crystallographic waters in this particular protein are bridged to the outside protein surface via a series of progressively more accessible water sites. On the surface of the protein, water molecules exchange quickly between crystallographic water sites. Time-averaging crystallographic refinement provides a view based on experimental data of the relative accessibility of water sites in and around a protein in a crystalline environment. Proteins 1999;36:501-511.

show abstract

A microscopic view of protein solvation

Cited by 35 publications

References 3 publications

Nucleation and Growth Mechanisms of Protein Crystals

Nucleation and Growth Mechanisms of Protein Crystals

Effects of dimerization of Serratia marcescens endonuclease on water dynamics

Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study

Contact Info

Product

Resources

About