Unraveling hot spots in binding interfaces: Progress and challenges

Current Opinion in Structural Biology

Volumn 12, Issue 1, 2002, Pages 14-20

  DeLano, Warren L ^a  

^a Sunesis Pharmaceuticals Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE;

ALGORITHM; BIOASSAY; BIOPHYSICS; DATA BASE; ENERGY TRANSFER; METHODOLOGY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MUTAGENESIS; MUTAGENICITY; PLASTICITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; REVIEW; STIMULATION; TECHNIQUE; THEORETICAL MODEL;

EID: 0036469060     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00283-X     Document Type: Review

References (49)

1. A hot spot of binding energy in a hormone-receptor interface
2. ASEdb: A database of alanine mutations and theireffects on the free energy of binding in protein interactions
3. Anatomy of hot spots in protein interfaces
4. The atomic structure of protein-protein recognition sites
5. Conservation of polar residues as hot spots at protein interfaces
6. Principles of protein-protein interactions
7. Side-chain flexibility in proteins upon ligand binding
8. Convergent solutions to binding at a protein-protein interface
9. The peroxisomal membrane protein Pex13p shows a novel mode of SH3 interaction
10. Energetic determinants of internal motif recognition by PDZ domains
11. Protein functional epitopes: Hot spots, dynamics and combinatorial libraries
12. Understanding proteinfolding via free-energy surfaces from theory and experiment
13. Folding and binding cascades: Dynamic landscapes and population shifts
14. Wet and dry interfaces: The role of solvent in protein-protein and protein-DNA recognition
15. May the driving force be with you - Whatever it is
16. Structural response to mutation at a protein-protein interface
17. Structural evidence for recognition of a single epitope by two distinct antibodies
18. Alanine scanning mutants of rat proinsulin I show functional diversity of anti-insulin monoclonal antibodies
19. Epitope mapping for four monoclonal antibodies against human plasminogen activator inhibitor type-1: Implications for antibody-mediated PAI-1-neutralization and vitronectin-binding
20. Evidence that a protein-protein interaction 'hot spot' on heterotrimeric G protein βγ subunits is used for recognition of a subclass of effectors
21. A novel family of hairpin peptides that inhibit IgE activity by binding to the high-affinity IgE receptor
22. Structure-function analysis of a phage display-derived peptide that binds to insulin-like growth factor binding protein 1
23. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
24. Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions
25. Theoretical studies suggest a new antifolate as a more potent inhibitor of thymidylate synthase
26. Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides
27. Improved scoring of ligand-protein interactions using OWFEG free energy grids
28. Computationally accessible method for estimating free energy changes resulting from site-specific mutations of biomolecules: Systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins
29. Modeling implicit reorganization in continuum descriptions of protein-protein interactions
30. Evaluation of protein-protein association energies by free energy perturbation calculations
31. Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior
32. An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis
33. Dissection of a nuclear localization signal
34. Crystal structure of a neutralizing human IgG against HIV-1: A template for vaccine design
35. Lysine 322 in the human IgG3 C(H)2 domain is crucial for antibody dependent complement activation
36. New structural and functional aspects of the type I interferon-receptor interaction revealed by comprehensive mutational analysis of the binding interface
37. Identification of the ligand-binding site of the BMP type IA receptor for BMP-4
38. + channel
39. Development of laminin receptor agonists: Identification of important functional residues by alanine scanning
40. Functional significance of the beta hairpin in the insecticidal neurotoxin omega-atracotoxin-Hv1a
41. N-terminal residues of plasmatocyte spreading peptide possess specific determinants required for biological activity
42. A binding pocket for a small molecule inhibitor of HIV-1 entry within the transmembrane helices of CCR5
43. Scanning mutagenesis identifies amino acid side chains in transmembrane domain 5 of the M(1) muscarinic receptor that participate in binding the acetyl methyl group of acetylcholine
44. Fast transient cytokine-receptor interactions monitored in real time by reflectometric interference spectroscopy
45. Rapid mapping of protein functional epitopes by combinatorial alanine scanning
46. Site-directed ligand discovery
47. Analysis of the interactions of human ribonuclease inhibitor with angiogenin and ribonuclease A by mutagenesis: Importance of inhibitor residues inside versus outside the C-terminal 'hot spot'