Exploring steric constraints on protein mutations using MAGE/PROBE

Protein Science

Volumn 9, Issue 11, 2000, Pages 2251-2259

  Word, J Michael ^a,c   Presley, Brent K ^a,d   Lovell, Simon C ^a   Richardson, David C ^a   Batemanm, Robert C ^b  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b The University of Southern Mississippi   (United States)

^c GLAXOSMITHKLINE   (United States)

^d UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

All atom contact analysis; Explicit hydrogens; Interactive molecular graphics; Kinemages; Side chain conformational maps; Site directed mutagenesis

Indexed keywords

LEUCINE; LYSOZYME; MUTANT PROTEIN; RICIN;

ARTICLE; COMPUTER PROGRAM; CONFORMATIONAL TRANSITION; ENZYME ACTIVITY; GENE MUTATION; GENE PROBE; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS; STEREOCHEMISTRY;

EID: 0034487752     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.9.11.2251     Document Type: Article

References (43)

1. The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme
2. Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme
3. The Protein Data Bank
4. The Protein Data Bank: A computer-based archival file for macromolecular structures
5. Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala → Ser and Val → Thr substitutions in T4 lysozyme
6. Determination of alpha-helix propensity within the context of a folded protein
7. Structural basis of amino acid alpha helix propensity
8. The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes
9. Accurate bond and angle parameters for X-ray protein structure refinement
10. Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences
11. A mutant T4 lysozyme displays 5 different crystal conformations
12. Selection and characterization of ricin toxin A-chain mutations in Saccharomyces cerevisiae
13. Role of arginine 180 and glutamic acid 177 of ricin toxin A chain in enzymatic inactivation of ribosomes
14. A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme
15. Folding kinetics of a fluorescent variant of monomeric λ repressor
16. Evidence that glutamic acid 167 is an active-site residue of Shiga-like toxin I
17. Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme
18. Hydrophobic packing in T4 lysozyme probed by cavity-filling mutants
19. Structure of a ricin mutant showing rescue of activity by a noncatalytic residue
20. Real-time color graphics in studies of molecular interactions
21. Prediction of protein side-chain conformation by packing optimization
22. Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme
23. The penultimate rotamer library
24. A transmembrane helix dimer: Structure and implications
25. Control of enzyme activity by an engineered disulfide bond
26. Studies on protein stability with T4 lysozyme
27. Structure of recombinant ricin A chain at 2.3 Å
28. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic changes, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
29. GRASP-Graphical representation and analysis of surface-properties
30. Protein sidechain conformer prediction: A test of the energy function
31. Spherical shading
32. The kinemage: A tool for scientific illustration
33. Kinemages - Simple macromolecular graphics for interactive teaching and publication
34. MAGE, PROBE, and Kinemages
35. Role of glutamic acid 177 of the ricin toxin A chain in enzymatic inactivation of ribosomes
36. Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme
37. X-ray structure of recombinant ricin A-chain at 1.8Å resolution
38. Evaluation of the resultant van der Waals interactions after modeling the cleavage site phosphate into the crystal structure of the HDV genomic ribozyme
39. Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogens
40. Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
41. Protein-protein recognition: An experimental and computational study of the R89K mutation in Raf and its effect on Ras binding