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Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme
- Source :
- Protein science : a publication of the Protein Society, vol 10, iss 5, Xu, J; Baase, WA; Quillin, ML; Baldwin, EP; & Matthews, BW. (2001). Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme. PROTEIN SCIENCE, 10(5), 1067-1078. doi: 10.1110/ps.02101. UC Davis: Retrieved from: http://www.escholarship.org/uc/item/92z0t5kk
- Publication Year :
- 2001
- Publisher :
- Cold Spring Harbor Laboratory Press, 2001.
-
Abstract
- To investigate the structural and thermodynamic basis of the binding of solvent at internal sites within proteins a number of mutations were constructed in T4 lysozyme. Some of these were designed to introduce new solvent-binding sites. Others were intended to displace solvent from preexisting sites. In one case Val-149 was replaced with alanine, serine, cysteine, threonine, isoleucine, and glycine. Crystallographic analysis shows that, with the exception of isoleucine, each of these substitutions results in the binding of solvent at a polar site that is sterically blocked in the wild-type enzyme. Mutations designed to perturb or displace a solvent molecule present in the native enzyme included the replacement of Thr-152 with alanine, serine, cysteine, valine, and isoleucine. Although the solvent molecule was moved in some cases by up to 1.7 A, in no case was it completely removed from the folded protein. The results suggest that hydrogen bonds from the protein to bound solvent are energy neutral. The binding of solvent to internal sites within proteins also appears to be energy neutral except insofar as the bound solvent may prevent a loss of energy due to potential hydrogen bonding groups that would otherwise be unsatisfied. The introduction of a solvent-binding site appears to require not only a cavity to accommodate the water molecule but also the presence of polar groups to help satisfy its hydrogen-bonding potential. It may be easier to design a site to accommodate two or more water molecules rather than one as the solvent molecules can then hydrogen-bond to each other. For similar reasons it is often difficult to design a point mutation that will displace a single solvent molecule from the core of a protein.
- Subjects :
- Steric effects
Models, Molecular
Protein Conformation
water
Biophysics
T4 lysozyme
Crystallography, X-Ray
Biochemistry
Article
Protein structure
Models
Enzyme Stability
Molecule
Bacteriophage T4
Point Mutation
Binding site
Other Information and Computing Sciences
Molecular Biology
Crystallography
Binding Sites
Hydrogen bond
Chemistry
cavities
Molecular
Water
Computation Theory and Mathematics
Hydrogen Bonding
Solvent
A-site
Amino Acid Substitution
hydrogen bonds
X-Ray
Solvents
Thermodynamics
Muramidase
Biochemistry and Cell Biology
Isoleucine
hydration
Protein Binding
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Protein science : a publication of the Protein Society, vol 10, iss 5, Xu, J; Baase, WA; Quillin, ML; Baldwin, EP; & Matthews, BW. (2001). Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme. PROTEIN SCIENCE, 10(5), 1067-1078. doi: 10.1110/ps.02101. UC Davis: Retrieved from: http://www.escholarship.org/uc/item/92z0t5kk
- Accession number :
- edsair.doi.dedup.....aa9831241ebf5a28f2f67fbae8e5183c
- Full Text :
- https://doi.org/10.1110/ps.02101.