CoChat
Sign Up
Cited by 93Protein Structure and DynamicsEnzyme Structure and Functionthermodynamics and calorimetric analyses

Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala.fwdarw, ser and Val.fwdarw. Thr substitutions in T4 lysozyme.

Blaber, Michael, Lindstrom, Joel D., Gassner, Nadine, Xu, Jian, Heinz, Dirk W., Matthews, Brian W.·1993·Biochemistry
DOI 10.1021/bi00093a013
Open this paper in CoChat — free account

Abstract

In order to determine the thermodynamic cost of introducing a polar group within the core of a protein, a series of nine Ala-->Ser and 3 Val-->Thr substitutions was constructed in T4 lysozyme. The sites were all within alpha-helices but ranged from fully solvent-exposed to totally buried. The range of destabilization incurred by the Ala-->Ser substitutions was found to be very similar to that for the Val-->Thr replacements. For the solvent-exposed and partly exposed sites the destabilization was modest (approximately less than 0.5 kcal/mol). For the completely buried sites the destabilization was larger, but variable (approximately 1-3 kcal/mol). Crystal structure determinations showed that the Ala-->Ser mutant structures were, in general, very similar to their wild-type counterparts, even though the replacements introduce a hydroxyl group. This is in part because the introduced serines are all within alpha-helices and at congested sites can avoid steric clashes with surrounding atoms by making a hydrogen bond to a backbone carbonyl oxygen in the preceding turn of the helix. The three substituted threonine side chains essentially superimpose on their valine counterparts but display somewhat larger conformational adjustments. The results illustrate how a protein structure will adapt in different ways to avoid the presence of an unsatisfied hydrogen bond donor or acceptor. In the most extreme case, Val 149-->Thr, which is also the most destabilizing variant (delta delta G = 2.8 kcal/mol), a water molecule is incorporated in the mutant structure in order to provide a hydrogen-bonding partner. The results are consistent with the view that many hydrogen bonds within proteins contribute only marginally to stability but that noncharged polar groups that lack a hydrogen-bonding partner are very destabilizing (delta delta G approximately greater than 3 kcal/mol). Supportive of other studies, the alpha-helix propensity of alanine is seen to be higher than that of serine (delta delta G = 0.46 +/- 0.04 kcal/mol), while threonine and valine are similar in alpha-helix propensity.

Integrity signals

Registry

Crossref · 10.1021/bi00093a013

Cites

45 of 45 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The desolvation of polar or charged groups of the protein or ligand is unfavorable to binding when the formed solute-solvent interactions are not effectively satisfied upon protein-ligand binding.

    “At the same time, the desolvation of polar or charged groups of the protein or ligand is unfavorable to binding when the formed solute–solvent interactions are not effectively satisfied upon the protein–ligand binding (Blaber et al., 1993; Kar et al., 2013).”

    From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Blaber et al., 1993

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Related

Authors
Blaber, M., Lindstrom, J. D., Gassner, N., Xu, J., Heinz, D. W., & Matthews, B. W.
Affiliations
Howard Hughes Medical Institute (US)
ORCID
Venue
Biochemistry
Publisher
American Chemical Society (ACS)
Published
1993-10-01
Volume
32
Issue
42
Pages
11363-11373
ISSN
  • 0006-2960 (ISSN-L)
  • 1520-4995
DOI
10.1021/bi00093a013
OpenAlex
W2064168223
Cited by
93
References
45
Citations by year
2025: 2 · 2021: 1 · 2018: 3 · 2017: 2 · 2016: 1 · 2014: 3 · 2013: 2 · 2012: 3
FWCI
2.43
Type
journal article
Language
en
Open access
closed
Locations
  • Biochemistry (publishedVersion)
  • PubMed (publishedVersion)
Funders
National Institute of General Medical Sciences (GM-21967, R01GM021967)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › thermodynamics and calorimetric analyses
Keywords
T4 lysozyme, buried residues, alpha-helix propensity, hydrogen bonding, protein stability, side-chain conformation
MeSH terms
Alanine, Amino Acid Sequence, Calorimetry, Circular Dichroism, Enzyme Stability, Models, Molecular, Muramidase, Recombinant Proteins, Serine, Threonine, Valine, Mutagenesis, Site-Directed, Bacteriophage T4, Point Mutation, Protein Structure, Secondary

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review