1L60

ANALYSIS OF THE INTERACTION BETWEEN CHARGED SIDE CHAINS AND THE ALPHA-HELIX DIPOLE USING DESIGNED THERMOSTABLE MUTANTS OF PHAGE T4 LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Analysis of the effectiveness of proline substitutions and glycine replacements in increasing the stability of phage T4 lysozyme.

Nicholson, H.Tronrud, D.E.Becktel, W.J.Matthews, B.W.

(1992) Biopolymers 32: 1431-1441

  • DOI: 10.1002/bip.360321103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • It was previously shown that the two replacements Gly 77-->Ala (G77A) and Ala 82-->Pro (A82P) increase the thermostability of phage T4 lysozyme at pH 6.5. Such replacements are presumed to restrict the degrees of freedom of the unfolded protein and s ...

    It was previously shown that the two replacements Gly 77-->Ala (G77A) and Ala 82-->Pro (A82P) increase the thermostability of phage T4 lysozyme at pH 6.5. Such replacements are presumed to restrict the degrees of freedom of the unfolded protein and so decrease the entropy of unfolding [B. W. Matthews, H. Nicholson, and W. J. Becktel (1987) Proceedings of the National Academy of Science USA Vol. 84, pp. 6663-6667]. To further test this approach, three additional replacements--G113A, K60P and A93P--have been constructed. On the basis of model building, each of these three replacements was judged to be less than optimal because it would tend to introduce unfavorable van der Waals contacts with neighboring parts of the protein. The presence of such contacts was verified for G113A and K60P by conformational adjustments seen in the crystal structures of these mutant proteins. In the case of G113A there are backbone conformational changes of 0.5-1.0 A in the short alpha-helix, 108-113, that includes the site of substitution. In the case of K60P the pyrrolidine ring shows evidence of strain. The thermal stability of each of the three variants at both pH 2.0 and pH 6.5 was found to be very close to that of wild-type lysozyme. The results suggest that the procedure used to predict sites for both Xaa-->Pro and Gly-->Ala is, in principle, correct. At the same time, the increase in stability expected from substitutions of this type is modest, and can easily be offset by strain associated with introduction of the alanine or proline. This means that the criteria used to select substitutions that will increase thermostability have to be stringent at least. In the case of T4 lysozyme this severely limits the number of sites. The analysis reveals a significant discrepancy between the conformational energy surface predicted for the residue preceding a proline and the conformations observed in crystal structures.


    Related Citations: 
    • Replacements of Pro86 in Phage T4 Lysozyme Extend an Alpha-Helix But Do not Alter Protein Stability
      Alber, T.,Bell, J.A.,Dao-Pin, S.,Nicholson, H.,Cook, J.A.Wozniak S.,Matthews, B.W.
      (1988) Science 239: 631
    • Enhanced Protein Thermostability from Site-Directed Mutations that Decrease the Entropy of Unfolding
      Matthews, B.W.,Nicholson, H.,Becktel, W.J.
      (1987) Proc.Natl.Acad.Sci.USA 84: 6663
    • Crystallographic Determination of the Mode of Binding of Oligosaccharides to T4 Bacteriophage Lysozyme. Implications for the Mechanism of Catalysis
      Anderson, W.F.,Gruetter, M.G.,Remington, S.J.,Weaver, L.H.,Matthews, B.W.
      (1981) J.Mol.Biol. 147: 523
    • The Structural and Thermodynamic Consequences of Burying a Charged Residue within the Hydrophobic Core of T4 Lysozyme
      Daopin, S.,Anderson, E.,Baase, W.,Dahlquist, F.W.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • Structural and Thermodynamic Analysis of the Packing of Two Alpha-Helices in Bacteriophage T4 Lysozyme
      Daopin, S.,Alber, T.,Baase, W.A.,Wozniak, J.A.,Matthews, B.W.
      (1991) J.Mol.Biol. 221: 647
    • Contributions of Engineered Surface Salt Bridges to the Stability of T4 Lysozyme Determined by Directed Mutagenesis
      Dao-Pin, S.,Sauer, U.,Nicholson, H.,Matthews, B.W.
      (1991) Biochemistry 30: 7142
    • Analysis of the Interaction between Charged Side Chains and the Alpha-Helix Dipole Using Designed Thermostable Mutants of Phage T4 Lysozyme
      Nicholson, H.,Anderson, D.E.,Dao-Pin, S.,Matthews, B.W.
      (1991) Biochemistry 30: 9816
    • Cumulative Site-Directed Charge-Change Replacements in Bacteriophage T4 Lysozyme Suggest that Long-Range Electrostatic Interactions Contribute Little to Protein Stability
      Dao-Pin, S.,Soderlind, E.,Baase, W.A.,Wozniak, J.A.,Sauer, U.,Matthews, B.W.
      (1991) J.Mol.Biol. 221: 873
    • High-Resolution Structure of the Temperature-Sensitive Mutant of Phage Lysozyme, Arg 96 (Right Arrow) His
      Weaver, L.H.,Gray, T.M.,Gruetter, M.G.,Anderson, D.E.,Wozniak, J.A.,Dahlquist, F.W.,Matthews, B.W.
      (1989) Biochemistry 28: 3793
    • Structure of a Thermostable Disulfide-Bridge Mutant of Phage T4 Lysozyme Shows that an Engineered Crosslink in a Flexible Region Does not Increase the Rigidity of the Folded Protein
      Pjura, P.E.,Matsumura, M.,Wozniak, J.A.,Matthews, B.W.
      (1990) Biochemistry 29: 2592
    • Enhanced Protein Thermostability from Designed Mutations that Interact with Alpha-Helix Dipoles
      Nicholson, H.,Becktel, W.J.,Matthews, B.W.
      (1988) Nature 336: 651
    • Structural Analysis of the Temperature-Sensitive Mutant of Bacteriophage T4 Lysozyme, Glycine 156 (Right Arrow) Aspartic Acid
      Gray, T.M.,Matthews, B.W.
      (1987) J.Biol.Chem. 262: 16858
    • Relation between Hen Egg White Lysozyme and Bacteriophage T4 Lysozyme. Evolutionary Implications
      Matthews, B.W.,Remington, S.J.,Gruetter, M.G.,Anderson, W.F.
      (1981) J.Mol.Biol. 147: 545
    • The Three Dimensional Structure of the Lysozyme from Bacteriophage T4
      Matthews, B.W.,Remington, S.J.
      (1974) Proc.Natl.Acad.Sci.USA 71: 4178
    • Multiple Stabilizing Alanine Replacements within Alpha-Helix 126-134 of T4 Lysozyme Have Independent, Additive Effects on Both Structure and Stability
      Zhang, X.-J.,Baase, W.A.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • Contributions of Left-Handed Helical Residues to the Structure and Stability of Bacteriophage T4 Lysozyme
      Nicholson, H.,Soderlind, E.,Tronrud, D.E.,Matthews, B.W.
      (1989) J.Mol.Biol. 210: 181
    • Tolerance of T4 Lysozyme to Multiple Xaa (Right Arrow) Ala Substitutions: A Polyalanine Alpha-Helix Containing Ten Consecutive Alanines
      Heinz, D.W.,Baase, W.A.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • Structural Studies of Mutants of the Lysozyme of Bacteriophage T4. The Temperature-Sensitive Mutant Protein Thr157 (Right Arrow) Ile
      Gruetter, M.G.,Gray, T.M.,Weaver, L.H.,Alber, T.,Wilson, K.,Matthews, B.W.
      (1987) J.Mol.Biol. 197: 315
    • Structural Studies of Mutants of T4 Lysozyme that Alter Hydrophobic Stabilization
      Matsumura, M.,Wozniak, J.A.,Dao-Pin, S.,Matthews, B.W.
      (1989) J.Biol.Chem. 264: 16059
    • Atomic Coordinates for T4 Phage Lysozyme
      Remington, S.J.,Teneyck, L.F.,Matthews, B.W.
      (1977) Biochem.Biophys.Res.Commun. 75: 265
    • Toward a Simplification of the Protein Folding Problem: A Stabilizing Polyalanine Alpha-Helix Engineered in T4 Lysozyme
      Zhang, X.-J.,Baase, W.A.,Matthews, B.W.
      (1991) Biochemistry 30: 2012
    • Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
      Weaver, L.H.,Matthews, B.W.
      (1987) J.Mol.Biol. 193: 189
    • Common Precursor of Lysozymes of Hen Egg-White and Bacteriophage T4
      Matthews, B.W.,Gruetter, M.G.,Anderson, W.F.,Remington, S.J.
      (1981) Nature 290: 334
    • Tolerance of T4 Lysozyme to Proline Substitutions within the Long Interdomain Alpha-Helix Illustrates the Adaptability of Proteins to Potentially Destabilizing Lesions
      Sauer, U.H.,Dao-Pin, S.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • Temperature-Sensitive Mutations of Bacteriophage T4 Lysozyme Occur at Sites with Low Mobility and Low Solvent Accessibility in the Folded Protein
      Alber, T.,Dao-Pin, S.,Nye, J.A.,Muchmore, D.C.,Matthews, B.W.
      (1987) Biochemistry 26: 3754
    • Crystallographic Data for Lysozyme from Bacteriophage T4
      Matthews, B.W.,Dahlquist, F.W.,Maynard, A.Y.
      (1973) J.Mol.Biol. 78: 575
    • Contributions of Hydrogen Bonds of Thr 157 to the Thermodynamic Stability of Phage T4 Lysozyme
      Alber, T.,Dao-Pin, S.,Wilson, K.,Wozniak, J.A.,Cook, S.P.,Matthews, B.W.
      (1987) Nature 330: 41
    • Structure of the Lysozyme from Bacteriophage T4, an Electron Density Map at 2.4 Angstroms Resolution
      Remington, S.J.,Anderson, W.F.,Owen, J.,Teneyck, L.F.,Grainger, C.T.,Matthews, B.W.
      (1978) J.Mol.Biol. 118: 81
    • Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme
      Matthews, B.W.
      (1975) Biochim.Biophys.Acta 405: 442
    • Hydrophobic Stabilization in T4 Lysozyme Determined Directly by Multiple Substitutions of Ile 3
      Matsumura, M.,Becktel, W.J.,Matthews, B.W.
      (1988) Nature 334: 406


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute, Eugene, Oregon.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T4 LYSOZYME
A
164Enterobacteria phage T4Mutation(s): 0 
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.000α = 90.00
b = 61.000β = 90.00
c = 96.900γ = 120.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other