Random Coil to Globular Thermal Response (H3.1) Figure 7. Variation of the structure factor, S(q) , of histone H3.1 with the wave vector, q with MJ, BT, and BFKV potentials from simulations on a 643 lattice with 150 independent samples with t = 107 MCS time. doi:10.1371/journal.pone.0049352.g007 Author Contributions Conceived and designed the experiments: RBP BLF. Performed the experiments: RBP. Analyzed the data: RBP. Contributed reagents/ materials/analysis tools: RBP. Wrote the paper: RBP. References 1. Tanaka S, Scheraga HA (1976) Medium and long range interaction parameters between amino acids for predicting three dimensional structures of proteins. Macromolecules 9: 945–950. 2. Miyazawa S, Jernigan RL (1985) Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18: 534–552. 3. Miyazawa S, Jernigan RL (1996) Residue-residue potentials with a favorable contact pair term for simulation and treading. J Mol Biol 256: 623–644. 4. Residue-residue interaction tables website, courtesy of the research group of R.L. Jernigan. Available: http://gor.bb.iastate.edu/potential/. Accessed 2012 Oct 10. 5. Bagci Z, Kloczkowski A, Jernigan RL, Bahar I (2003) The Origin and Extent of Coarse Grained Irregularities in Protein Internal Packing I. Proteins 53: 56–67. 6. Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA (1993) Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide- group dipole alignment. Prot Sci 2: 1697–1714. 7. Betancourt MR, Thirumalai D (1999) Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 2: 361–369. 8. Bastolla U, Farwer J, Knapp EW, Vendruscolo M (2001) How to guarantee optimal stability for most representative structures in the proten data bank. Proteins 44: 79–96. 9. Maiorov VN, Crippen GM (1992) Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 227: 876–888. 10. Godzik A, Kolinski A, Skolnick J (1996) Knowledge-based potentials for protein folding: what can we learn from protein structures? Proteins 4: 363–366. 11. Skolnick J, Jaroszewski L, Kolinski A (1997) Derivation and testing of pair potentials for protein folding: When is the quasichemical approximation correct? Protein Sci 6: 676–688. 12. Hinds DA, Levitt M (1992) A lattice model for protein structure prediction at low resolution. Proc Natl Acad Sci USA 89: 2536–2540. 13. Fiebig KM, Dill KA (1993) Protein Core Assembly Processes. J Chem Phys 98: 3475–3487. 14. Bryant SH, Lawrence CE (1993) An empirical energy function for threading protein sequence through folding motif. Proteins 16: 92–112. 15. Wolynes PG, Onuchic JN,Thirumalai D (1995) Navigating the folding routes. Science 267: 1619–1620. 16. Tobi D, Shafran G, Linial N, Elber R (2000) On the design and analysis of protein folding potentials. Proteins 40: 71–85. PLOS ONE | www.plosone.org 8 November 2012 | Volume 7 | Issue 11 | e49352