ArticleBiophysical journal2008
Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 35 citations in OpenAlex.
- Article
- Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields.Journal of chemical theory and computation · 2024Article
- Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants.Journal of the American Chemical Society · 2022Article
- Quantifying charge state heterogeneity for proteins with multiple ionizable residues.Biophysical journal · 2021Article
- Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo.Journal of computer-aided molecular design · 2021Article
- Cancer and pH Dynamics: Transcriptional Regulation, Proteostasis, and the Need for New Molecular Tools.Cancers · 2020Review
- Water in protein hydration and ligand recognition.Journal of molecular recognition : JMR · 2019Review
- Article
- Lessons from pressure denaturation of proteins.Journal of the Royal Society, Interface · 2018Review
- Large-scale crystallization and neutron crystallographic analysis of HSP70 in complex with ADP.Acta crystallographica. Section F, Structural biology communications · 2017Article
- Arginine: Its pKa value revisited.Protein science : a publication of the Protein Society · 2015Article
- Characterization of a novel water pocket inside the human Cx26 hemichannel structure.Biophysical journal · 2014Article
- Structural reorganization triggered by charging of Lys residues in the hydrophobic interior of a protein.Structure (London, England : 1993) · 2012Article
- Review
- Large shifts in pKa values of lysine residues buried inside a protein.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Structural origins of high apparent dielectric constants experienced by ionizable groups in the hydrophobic core of a protein.Journal of molecular biology · 2011Article
- High-pressure SAXS study of folded and unfolded ensembles of proteins.Biophysical journal · 2010Article
- Charges in the hydrophobic interior of proteins.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease.Biochemistry · 2010Article
- The pK(a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors.Journal of molecular biology · 2009Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Although internal water molecules are essential for the structure and function of many proteins, the structural and physical factors that govern internal hydration are poorly understood. We have examined the molecular determinants of internal hydration systematically, by solving the crystal structures of variants of staphylococcal nuclease with Gln-66, Asn-66, and Tyr-66 at cryo (100 K) and room (298 K) temperatures, and comparing them with existing cryo and room temperature structures of variants with Glu-66, Asp-66, Lys-66, Glu-92 or Lys-92 obtained under conditions of pH where the internal ionizable groups are in the neutral state. At cryogenic temperatures the polar moieties of all these internal side chains are hydrated except in the cases of Lys-66 and Lys-92. At room temperature the internal water molecules were observed only in variants with Glu-66 and Tyr-66; water molecules in the other variants are probably present but they are disordered and therefore undetectable crystallographically. Each internal water molecule establishes between 3 and 5 hydrogen bonds with the protein or with other internal water molecules. The strength of interactions between internal polar side chains and water molecules seems to decrease from carboxylic acids to amides to amines. Low temperature, low cavity volume, and the presence of oxygen atoms in the cavity increase the positional stability of internal water molecules. This set of structures and the physical insight they contribute into internal hydration will be useful for the development and benchmarking of computational methods for artificial hydration of pockets, cavities, and active sites in proteins.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.