Coevolution signals capture the specific packing of secondary structures in protein architecture

References

[1] Acharya A, Rishi V, Vinson C (2006) Stability of 100 homo and heterotypic coiled-coil a-a′ pairs for ten amino acids (A, L, I, V, N, K, S, T, E, and R). Biochemistry45: 11324-11332

[2] Cheng J, Baldi P (2005) Three-stage prediction of protein betasheets by neural networks, alignments and graph algorithms. Bioinformatics21(Suppl 1): i75-i84

[3] DeLong ER, DeLong DM, Clarke-Pearson DL (1988) Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics44: 837-845

[4] Levitt M, Chothia C (1976) Structural patterns in globular proteins. Nature261: 552-558

[5] Liang Y, Pingali SV, Jogalekar AS, Snyder JP, Thiyagarajan P, Lynn DG (2008) Cross-strand pairing and amyloid assembly. Biochemistry47: 10018-10026

[6] Lippi M, Frasconi P (2009) Prediction of protein beta-residue contacts by Markov logic networks with grounding-specific weights. Bioinformatics25: 2326-2333

[7] Matousek WM, Ciani B, Fitch CA, Garcia-Moreno B, Kammerer RA, Alexandrescu AT (2007) Electrostatic contributions to the stability of the GCN4 leucine zipper structure. J Mol Biol374: 206-219

[8] Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol247: 536-540

[9] Oakley MG, Kim PS (1998) A buried polar interaction can direct the relative orientation of helices in a coiled coil. Biochemistry37: 12603-12610

[10] Phillips ST, Piersanti G, Bartlett PA (2005) Quantifying amino acid conformational preferences and side-chain-side-chain interactions in beta-hairpins. Proc Natl Acad Sci USA102: 13737-13742

[11] Ryan SJ, Kennan AJ (2007) Variable stability heterodimeric coiledcoils from manipulation of electrostatic interface residue chain length. J Am Chem Soc129: 10255-10260

[12] Schneider A, Dessimoz C, Gonnet GH (2007) OMA Browser—exploring orthologous relations across 352 complete genomes. Bioinformatics23: 2180-2182

[13] Smith CK, Regan L (1995) Guidelines for protein design—the energetics of beta-sheet side-chain interactions. Science270: 980-982

[14] Steward RE, Thornton JM(2002) Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory. Proteins-Struct Funct Bioinf48: 178-191

[15] Woolfson DN (2005) The design of coiled-coil structures and assemblies. In: Parry DAD, Squire JM(eds) Fibrous proteins: coiled-coils, collagen and elastomers. Elsevier Academic Press Inc., San Diego, pp 79-112

RIGHTS & PERMISSIONS

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.