Emergence of highly designable protein-backbone conformations in an off-lattice model

Proteins: Structure, Function and Genetics

Volumn 47, Issue 4, 2002, Pages 506-512

  Miller, Jonathan ^a   Zeng, Chen ^a   Wingreen, Ned S ^a   Tang, Chao ^a  

^a NEC LABORATORIES AMERICA   (United States)

Author keywords

Design ability; Evolution; Off lattice model; Protein design; Protein folds

Indexed keywords

HELIX LOOP HELIX PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; THERMODYNAMICS; ZINC FINGER MOTIF;

AMINO ACID MOTIFS; AMINO ACIDS; ANIMALS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 0036606863     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10107     Document Type: Article

References (38)

1. Protein design: The choice of de novo sequences
2. Functionalization of designed folded polypeptides
3. The current state and prospect of de novo protein design
4. Combinatorial protein design by in vitro recombination
5. Engineering and design: Recent adventures in molecular design - Editorial overview
6. Helical protein design
7. Protein design: A perspective from simple tractable models
8. De novo designa and structural characterization of proteins and metalloproteins
9. High-resolution protein design with backbone freedom
10. Design of a monomeric 23-residue polypeptide with defined tertiary structure
11. De novo protein design: Fully automated sequence selection
12. De novo protein design: Towards fully automated sequence selection
13. One thousand families for the molecular biologist
14. Emergence of preferred structures in a simple model of protein folding
15. Are protein folds atypical?
16. Searching for foldable protein structures using optimized energy functions
17. Why are some protein structures so common?
18. Why do globular proteins fit the limited set of folding patterns?
19. Forces of tertiary structural organization in globular proteins
20. Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study
21. The complexity and accuracy of discrete state models of protein structure
22. SERF: A program for accessible surface area calculations
23. Lattice statistical mechanics model of the conformational and sequence spaces of proteins
24. High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein
25. Contact order, transition state placement and the refolding rates of single domain proteins
26. Protein folding: Matching speed and locality
27. Variational theory for site resolved protein folding free energy surfaces
28. Finding the right fold
29. Matching theory and experiment in protein folding
30. Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
31. Role of secondary Motifs in fast folding polymers: A dynamical variational principle
32. A surprising simplicity to protein folding
33. Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
34. Sequence, stability, topology and length; the determinants of two-state protein folding kinetics
35. Protein design based on folding models
36. Folding of bovine pancreatic trypsin inhibitor (BPTI) variants in which almost half the residues are alanine
37. Tolerance of Arc repressor to multiple-alanine substitutions