Page 51 - Human Environment Interface (1)
P. 51
Anchored Design of Protein-Protein Interfaces
30. Liu S, Liu SY, Zhu XL, Liang HH, Cao AN, et al. (2007) Nonnatural protein- discovery. Nucleic Acids Research 38(suppl 2): W407–W411. 10.1093/nar/
protein interaction-pair design by key residues grafting. Proc Natl Acad Sci U S A gkq502.
104(13): 5330–5335. 42. Janin J (2010) Protein-protein docking tested in blind predictions: The CAPRI
experiment. Mol Biosyst 6(12): 2351–2362. 10.1039/c005060c.
31. Rohl CA, Strauss CEM, Misura KMS, Baker D (2004) Protein structure 43. Wallen JR, Paige C, Mallett TC, Karplus PA, Claiborne A (2008) Pyridine
prediction using rosetta. Methods Enzymol 383: 662+. nucleotide complexes with bacillus anthracis coenzyme A-disulfide reductase: A
structural analysis of dual NAD(P)H specificity. Biochemistry 47(18): 5182–5193.
32. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, et al. (2003) 10.1021/bi8002204.
Protein-protein docking with simultaneous optimization of rigid-body displace- 44. Stanfield RL, Dooley H, Verdino P, Flajnik MF, Wilson IA (2007) Maturation of
ment and side-chain conformations. J Mol Biol 331(1): 281–299. shark single-domain (IgNAR) antibodies: Evidence for induced-fit binding. J Mol
Biol 367(2): 358–372. 10.1016/j.jmb.2006.12.045.
33. Canutescu AA, Dunbrack RL (2003) Cyclic coordinate descent: A robotics 45. Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ (2005)
algorithm for protein loop closure. Protein Sci 12(5): 963–972. CAPRI rounds 3-5 reveal promising successes and future challenges for
RosettaDock. Proteins 60(2): 181–186.
34. Mandell DJ, Coutsias EA, Kortemme T (2009) Sub-angstrom accuracy in 46. Schmidt AE, Chand HS, Cascio D, Kisiel W, Bajaj SP (2005) Crystal structure
protein loop reconstruction by robotics-inspired conformational sampling. of kunitz domain 1 (KD1) of tissue factor pathway inhibitor-2 in complex with
Nature Methods 6(8): 551–552. 10.1038/nmeth0809-551. trypsin. implications for KD1 specificity of inhibition. J Biol Chem 280(30):
27832–27838. 10.1074/jbc.M504105200.
35. Coutsias EA, Seok C, Wester MJ, Dill KA (2006) Resultants and loop closure. 47. Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, et al. (2010)
International Journal of Quantum Chemistry 106(1): 176–189. -10.1002/ Rosetta in CAPRI rounds 13-19. Proteins 78(15): 3212–3218. 10.1002/
qua.20751. prot.22784.
48. Gulyani A, Vitriol E, Allen R, Wu J, Gremyachinskiy D, et al. A biosensor
36. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, et al. (2003) Design generated via high throughput screening quantifies cell edge src dynamics
of a novel globular protein fold with atomic-level accuracy. Science 302(5649): Nature Chemical Biology, In press.
1364–1368. 49. Rohl CA, Strauss CEM, Chivian D, Baker D (2004) Modeling structurally
variable regions in homologous proteins with rosetta. Proteins 55(3): 656–677.
37. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: Pattern 50. Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, et al. (2010)
recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12): Computational design of an enzyme catalyst for a stereoselective bimolecular
2577–2637. 10.1002/bip.360221211. diels-alder reaction. Science 329(5989): 309–313. 10.1126/science.1190239.
38. Clackson T, Wells JA (1995) A hot-spot of binding-energy in a hormone-
receptor interface. Science 267(5196): 383–386.
39. Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol
Biol 280(1): 1–9.
40. Kortemme T, Baker D (2002) A simple physical model for binding energy hot
spots in protein-protein complexes. Proc Natl Acad Sci U S A 99(22):
14116–14121.
41. Meireles LMC, Do¨mling AS, Camacho CJ (2010) ANCHOR: A web server and
database for analysis of protein–protein interaction binding pockets for drug
PLoS ONE | www.plosone.org 14 June 2011 | Volume 6 | Issue 6 | e20872
