Local Interactions in Protein Folding: Lessons from the α-Helix

INTRODUCTIONThe α-helix is an elegantly simple structure (1Pauling L. Corey R.B. Branson H.R. Proc. Natl. Acad. Sci. U. S. A. 1951; 37: 205-210Crossref PubMed Scopus (1908) Google Scholar), but helix thermodynamics has proven to be complex and often refractory. The appealing idea that helix formation is an early guiding event in protein folding (2Ptitsyn O.B. Rashin A.A. Biophys. Chem. 1975; 3: 1-20Crossref PubMed Scopus (193) Google Scholar, 3Levitt M. Chothia C. Nature. 1976; 261: 552-558Crossref PubMed Scopus (1083) Google Scholar, 4Cohen F.E. Richmond T.J. Richards F.M. J. Mol. Biol. 1979; 132: 275-288Crossref PubMed Scopus (127) Google Scholar, 5Rose G.D. J. Mol. Biol. 1979; 134: 447-470Crossref PubMed Scopus (203) Google Scholar, 6Baldwin R.L. Trends Biochem. Sci. 1989; 14: 291-294Abstract Full Text PDF PubMed Scopus (177) Google Scholar) remains controversial (7Chan H.S. Dill K.A. Proc. Natl. Acad. Sci. U. S. A. 1990; 87: 6388-6392Crossref PubMed Scopus (302) Google Scholar, 8Hunt N.G. Gregoret L.M. Cohen F.E. J. Mol. Biol. 1994; 241: 214-225Crossref PubMed Scopus (52) Google Scholar, 9Fersht A.R. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 10869-10873Crossref PubMed Scopus (456) Google Scholar, 10Zitzewitz J.A. Bilsel O. Luo J. Jones B.E. Matthews C.R. Biochemistry. 1995; 34: 12812-12819Crossref PubMed Scopus (188) Google Scholar, 11Sosnick T.R. Jackson S. Wilk R.R. Englander S.W. DeGrado W.F. Proteins Struct. Funct. Genet. 1996; 24: 427-432Crossref PubMed Scopus (111) Google Scholar). We suggest that the known facts are sufficient to resolve this controversy because they imply that side chain conformational entropy, and therefore helix propensity, must play an important organizing role during the earliest stages of protein folding.Briefly, the argument presented in this minireview is as follows. There are only two substantially populated conformers available to a non-glycyl/non-prolyl peptide (12Sasisekharan V. Ramanathan N. Collagen. John Wiley 23: 283-438Crossref PubMed Scopus (2745) Google Scholar), α and β, corresponding to regions of the ϕ,ψ map near (−60°,−40°) and (−120°,+135°), respectively. The repetition of α-values for successive residues results in a helix, a conformation that compacts the chain, thereby expelling water while engendering intrasegment hydrogen bonds (1Pauling L. Corey R.B. Branson H.R. Proc. Natl. Acad. Sci. U. S. A. 1951; 37: 205-210Crossref PubMed Scopus (1908) Google Scholar) and exquisite van der Waals contacts (14Makhatadze G.I. Privalov P.L. Adv. Protein Chem. 1995; 47: 307-425Crossref PubMed Scopus (996) Google Scholar). Although the peptide backbone has a strong tendency to leave the vapor phase and enter water (15Wolfenden R. Biochemistry. 1978; 17: 201-204Crossref PubMed Scopus (188) Google Scholar), the helix per se can be an even better "solvent" (16Murphy K.P. Gill S.J. J. Mol. Biol. 1991; 222: 699-709Crossref PubMed Scopus (264) Google Scholar). Further, water liberated by backbone polar groups upon helix formation is released, an entropically favored event.The preceding factors that promote helix formation are opposed by the entropic cost of freezing the main chain into a single conformation. On balance, helix formation must be energetically favorable for main chain atoms because alanine-based peptides are helical (17Marqusee S. Robbins V.H. Baldwin R.L. Proc. Natl. Acad. Sci. U. S. A. 1989; 86: 5286-5290Crossref PubMed Scopus (730) Google Scholar). Nonetheless, most peptides and protein segments are not helical, so unfavorable factors usually outweigh favorable ones. The several helix-promoting factors mentioned above all involve the peptide backbone and are therefore common to every residue (except glycine and proline). Consequently, helical conformation is the preferred state of the backbone (e.g. polyalanine), while helix-disfavoring factors must arise in the side chain.Side chains also pay an entropic price for helix formation because the presence of the bulky helix backbone is sterically incompatible with some side chain conformers (18Leach S.J. Nemethy G. Scheraga H.A. Biopolymers. 1966; 4: 369-407Crossref PubMed Scopus (105) Google Scholar, 19Creamer T.P. Rose G.D. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 5937-5941Crossref PubMed Scopus (301) Google Scholar). Unlike the backbone, where helix-affecting factors are the same from residue to residue, side chain entropy differs from one residue type to the next. For example, helix formation largely restricts a central valine to only one of its three possible side chain configurations because one of the γ-carbons "bumps" into a backbone atom in either of the other two. These side chain steric factors predispose segments of the chain toward either α or β regions of the ϕ,ψ map, and their influence would be exerted early in folding because the interactions are local, exerted between atoms that are close in sequence. Consecutive residues that preferentially populate the same region, either α or β, become candidates for further stabilization into helices or strands, respectively. These entropically driven segments of nascent secondary structure affect subsequent folding by favoring certain pathways and suppressing others. Thus, helix and strand formation will be guiding events in protein folding.The α-HelixThe α-helix (1Pauling L. Corey R.B. Branson H.R. Proc. Natl. Acad. Sci. U. S. A. 1951; 37: 205-210Crossref PubMed Scopus (1908) Google Scholar) is a well designed structure. Its hydrogen bonds are intrasegment and therefore self-contained, with near ideal geometry. Backbone atoms are close packed, and all interactions are local, confined between consecutive turns of the helix. Finally, the pattern is completely extensible; any number of consecutive residues can adopt a helical conformation with these favorable design characteristics.Helices are observed frequently in proteins (20Kabsch W. Sander C. Biopolymers. 1983; 22: 2577-2637Crossref PubMed Scopus (12108) Google Scholar), suggesting that the α-helix is also a stable structure. The autonomous stability of the helix has been a topic of keen interest for many years, motivated in part by conjectures about protein folding. One engaging idea has been that helices seed the folding pathway and influence later folding events. Unfortunately, early experimental evidence indicated that the cooperative unit for stable helix formation is ∼100 residues in length (21Sueki M. Lee S. Powers S.P. Denton J.B. Konishi Y. Scheraga H.A. Macromolecules. 1984; 17: 148-155Crossref Scopus (160) Google Scholar). This threshold exceeds the length of the average protein helix (∼12 residues (22Presta L.G. Rose G.D. Science. 1988; 240: 1632-1641Crossref PubMed Scopus (627) Google Scholar)) by almost an order of magnitude. Consequently, the conclusion that protein helices were far too short to function as independent folding units seemed inescapable.This prevailing view of the 1970s came to be reversed in the 1980s, after Bierzynski et al. (23Bierzynski A. Kim P.S. Baldwin R.L. Proc. Natl. Acad. Sci. U. S. A. 1982; 79: 2470-2474Crossref PubMed Scopus (276) Google Scholar), expanding upon earlier work by Brown and Klee (24Brown J.E. Klee W.A. Biochemistry. 1971; 10: 470-476Crossref PubMed Scopus (275) Google Scholar) demonstrated that residues 1-13 of ribonuclease, liberated upon cyanogen bromide cleavage, contained a helix that was stable in water at near physiological temperature. Other isolated protein fragments were found to be structured as well (25Dyson H.J. Rance M. Houghten R.A. Lerner R.A. Wright P.E. J. Mol. Biol. 1988; 201: 161-200Crossref PubMed Scopus (641) Google Scholar, 26Oas T.G. Kim P.S. Nature. 1988; 336: 42-48Crossref PubMed Scopus (248) Google Scholar). Such results prompted a re-evaluation; helices might function as independent folding units after all.What factors are responsible for helix stability (27Chakrabartty A. Baldwin R.L. Adv. Protein Chem. 1995; 46: 141-176Crossref PubMed Scopus (426) Google Scholar)? Two "textbook" features of helices are usually invoked to account for stability, hydrogen bonding (28Myers J.K. Pace C.N. Biophys. J. 1996; 71: 2033-2039Abstract Full Text PDF PubMed Scopus (252) Google Scholar) (but see 29Yang A.S. Honig B. J. Mol. Biol. 1995; 252: 351-365Crossref PubMed Scopus (225) Google Scholar) and tight main chain packing (14Makhatadze G.I. Privalov P.L. Adv. Protein Chem. 1995; 47: 307-425Crossref PubMed Scopus (996) Google Scholar). A third implicit feature is the fact that when the chain folds into a helix, bound water is released and returned to the bulk phase. These helix-promoting factors are opposed by the entropic cost of constraining the main chain to a single conformation. For backbone atoms, there appears to be a net tendency toward helix formation because alanine-based peptides (17Marqusee S. Robbins V.H. Baldwin R.L. Proc. Natl. Acad. Sci. U. S. A. 1989; 86: 5286-5290Crossref PubMed Scopus (730) Google Scholar, 30Chakrabartty A. Kortemme T. Baldwin R.L. Protein Sci. 1994; 3: 843-852Crossref PubMed Scopus (589) Google Scholar) are observed to be helical.What factors are responsible for helix specificity (27Chakrabartty A. Baldwin R.L. Adv. Protein Chem. 1995; 46: 141-176Crossref PubMed Scopus (426) Google Scholar, 31Lattman E.E. Rose G.D. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 439-441Crossref PubMed Scopus (155) Google Scholar)? That is, why are some peptides and protein segments helical, while others are not? The favorable main chain contributions to helix stability are constant from one residue to the next because all have identical backbones (except glycine and proline). Yet, most peptides are not helical nor are about 75% of the residues in proteins (20Kabsch W. Sander C. Biopolymers. 1983; 22: 2577-2637Crossref PubMed Scopus (12108) Google Scholar). Therefore, these helix-stabilizing main chain factors that cause polyalanine to be helical cannot be the ones that differentiate helix from non-helix.Helix capping has been hypothesized as a general mechanism that discriminates between helices and other conformational alternatives, including coil (22Presta L.G. Rose G.D. Science. 1988; 240: 1632-1641Crossref PubMed Scopus (627) Google Scholar, 32Richardson J.S. Richardson D.C. Science. 1988; 240: 1648-1652Crossref PubMed Scopus (1291) Google Scholar). In proteins, the helix of average length (∼12 residues) has eight intrasegment hydrogen bonds between successive amide hydrogen donors and carbonyl oxygen acceptors situated four residues previously in sequence (i.e. N-H(i) ··· O=C (i − 4)). Unavoidably, the initial four amide hydrogens and final four carbonyl oxygens of the helix lack intrasegment main chain hydrogen bonds because, upon termination, no next turn of helix exists to provide such partners. Thus, Pauling-Corey-Branson hydrogen bonds account for only 50% of the total in the helix of average length, with the first four N-H groups and last four C=O groups accounting for the remaining 50%.In both proteins and peptides, the chain leaving the helix tends to occlude some of these unsatisfied donors and acceptors, hindering access by solvent water. Provision of hydrogen bond partners for these otherwise unsatisfied amide hydrogens and carbonyl oxygens is termed helix capping. In addition to polar backbone groups, apolar side chains situated near helix termini can be solvent exposed, and therefore helix destabilizing, unless the chain folds so as to foster a hydrophobic contact. Recently, our definition of capping has been extended to include these hydrophobic capping interactions as well. 1R. Aurora and G. D. Rose, manuscript in preparation. The helix capping hypothesis has been confirmed experimentally in both peptides (34Bruch M.D. Dhingra M.M. Gierasch L.M. Proteins Struct. Funct. Genet. 1991; 10: 130-139Crossref PubMed Scopus (151) Google Scholar, 35Lyu P.C. Wemmer D.E. Zhou H.X. Pinker R.J. Kallenbach N.R. Biochemistry. 1993; 32: 421-425Crossref PubMed Scopus (134) Google Scholar, 36Forood B. Feliciano E.J. Nambiar K.P. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 838-842Crossref PubMed Scopus (223) Google Scholar, 37Chakrabartty A. Doig A.J. Baldwin R.L. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 11332-11336Crossref PubMed Scopus (212) Google Scholar) and proteins (38Serrano L. Fersht A.R. Nature. 1989; 342: 296-299Crossref PubMed Scopus (351) Google Scholar, 39Zhukovsky E.A. Mulkerrin M.G. Presta L.G. Biochemistry. 1994; 33: 9856-9864Crossref PubMed Scopus (41) Google Scholar). Recurrent capping motifs such as the capping box (40Dasgupta S. Bell J.A. Int. J. Pept. Protein Res. 1993; 41: 499-511Crossref PubMed Scopus (142) Google Scholar, 41Harper E.T. Rose G.D. Biochemistry. 1993; 32: 7605-7609Crossref PubMed Scopus (331) Google Scholar, 42Seale J.W. Srinivasan R. Rose G.D. Protein Sci. 1994; 3: 1741-1745Crossref PubMed Scopus (123) Google Scholar, 43Munoz V. Bianco F.J. Serrano L. Struct. Biol. 1995; 2: 380-385Crossref PubMed Scopus (129) Google Scholar) and the Schellman motif (44Schellman C. Jaenicke R. Protein Folding. Elsevier/North-Holland, Amsterdam1980: 53-61Google Scholar, 45Aurora R. Srinivasan R. Rose G.D. Science. 1994; 264: 1126-1130Crossref PubMed Scopus (265) Google Scholar), which contribute to the stability of protein helices (39Zhukovsky E.A. Mulkerrin M.G. Presta L.G. Biochemistry. 1994; 33: 9856-9864Crossref PubMed Scopus (41) Google Scholar), have been shown to persist in peptides (46Zhou H.X. Lyu P. Wemmer D.E. Kallenbach N.R. Proteins Struct. Funct. Genet. 1994; 18: 1-7Crossref PubMed Scopus (107) Google Scholar, 47Gong Y. Zhou H.X. Guo M. Kallenbach N.R. Protein Sci. 1995; 4: 1446-1456Crossref PubMed Scopus (37) Google Scholar), where they can inhibit expected fraying (48Zimm B.H. Bragg J.K. J. Chem. Phys. 1959; 31: 526-535Crossref Scopus (1668) Google Scholar) at helix ends.In 1990, individual residue contributions to helix stability were assessed in four separate host/guest systems (49Lyu P.C. Liff M.I. Marky L.A. Kallenbach N.R. Science. 1990; 250: 669-673Crossref PubMed Scopus (467) Google Scholar, 50O'Neil K.T. DeGrado W.F. Science. 1990; 250: 646-651Crossref PubMed Scopus (1115) Google Scholar, 51Padmanabhan S. Marqusee S. Ridgeway T. Laue T.M. Baldwin R.L. Nature. 1990; 344: 268-270Crossref PubMed Scopus (448) Google Scholar, 52Merutka G. Lipton W. Shalongo W. Park S.H. Stellwagen E. Biochemistry. 1990; 29: 7511-7515Crossref PubMed Scopus (135) Google Scholar). In such experiments, guest residues are substituted systematically at central positions (to avoid end effects) within a host peptide of known helical content and the resultant effect measured. Stabilizing substitutions increase helix content; destabilizing substitutions decrease it. An experimental scale of helix propensities is then derived by quantifying these effects in terms of the free energy differences (ΔΔG) between the stability of the host (ΔGhelix→coilhost) and each guest (ΔGhelix→coilguest). Although the host systems differed among these four groups, the resulting rank order of helix propensities was remarkably similar.What is the basis for these measured differences in helix propensity? Why does a small, nondescript residue like alanine have a higher helix propensity than valine? We hypothesized that the differences are due in large part to the loss of side chain conformational entropy upon helix formation (19Creamer T.P. Rose G.D. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 5937-5941Crossref PubMed Scopus (301) Google Scholar). Physically, this effect reflects the difference between the side chain's conformational freedom in the relatively flexible coil state and in the more restricted helical state, with its bulky helix backbone.We tested this hypothesis using Monte Carlo simulations (19Creamer T.P. Rose G.D. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 5937-5941Crossref PubMed Scopus (301) Google Scholar, 53Creamer T.P. Rose G.D. Proteins Struct. Funct. Genet. 1994; 19: 85-97Crossref PubMed Scopus (168) Google Scholar) and found that calculated entropy losses correlated strongly with experimental propensities in both peptides (49Lyu P.C. Liff M.I. Marky L.A. Kallenbach N.R. Science. 1990; 250: 669-673Crossref PubMed Scopus (467) Google Scholar, 50O'Neil K.T. DeGrado W.F. Science. 1990; 250: 646-651Crossref PubMed Scopus (1115) Google Scholar, 51Padmanabhan S. Marqusee S. Ridgeway T. Laue T.M. Baldwin R.L. Nature. 1990; 344: 268-270Crossref PubMed Scopus (448) Google Scholar, 52Merutka G. Lipton W. Shalongo W. Park S.H. Stellwagen E. Biochemistry. 1990; 29: 7511-7515Crossref PubMed Scopus (135) Google Scholar) and proteins (54Horovitz A. Matthews J.M. Fersht A.R. J. Mol. Biol. 1992; 227: 560-568Crossref PubMed Scopus (228) Google Scholar, 55Blaber M. Zhang X.J. Matthews B.W. Science. 1993; 260: 1637-1640Crossref PubMed Scopus (436) Google Scholar, 56Blaber M. Zhang X.J. Lindstrom J.D. Pepiot S.D. Baase W.A. Matthews B.W. J. Mol. Biol. 1994; 235: 600-624Crossref PubMed Scopus (183) Google Scholar). Related work by other groups reached similar conclusions (57Hermans J. Anderson A.G. Yun R.H. Biochemistry. 1992; 31: 5646-5653Crossref PubMed Scopus (101) Google Scholar, 60Wang J. Purisima E.O. J. Am. Chem. Soc. 1996; 118: 995-1001Crossref Scopus (44) Google Scholar).Conformational entropy is not the only proposed explanation for differences in helix specificity. Another is the drive to segregate polar and apolar residues on opposite helical faces, giving rise to an amphipathic helix (61Schiffer M. Edmundson A.B. Biophys. J. 1967; 7: 121-135Abstract Full Text PDF PubMed Scopus (898) Google Scholar, 62Segrest J.P. De Loof H. Dohlman J.G. Brouillette C.G. Anantharamaiah G.M. Proteins Struct. Funct. Genet. 1990; 8: 103-117Crossref PubMed Scopus (594) Google Scholar, 63Xiong H. Buckwalter B.L. Shieh H.-M. Hecht M.H. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 6349-6353Crossref PubMed Scopus (232) Google Scholar). While protein helices are often amphipathic, the host/guest peptide systems (49Lyu P.C. Liff M.I. Marky L.A. Kallenbach N.R. Science. 1990; 250: 669-673Crossref PubMed Scopus (467) Google Scholar, 50O'Neil K.T. DeGrado W.F. Science. 1990; 250: 646-651Crossref PubMed Scopus (1115) Google Scholar, 51Padmanabhan S. Marqusee S. Ridgeway T. Laue T.M. Baldwin R.L. Nature. 1990; 344: 268-270Crossref PubMed Scopus (448) Google Scholar, 52Merutka G. Lipton W. Shalongo W. Park S.H. Stellwagen E. Biochemistry. 1990; 29: 7511-7515Crossref PubMed Scopus (135) Google Scholar) are not. Therefore, amphipathic segregation is an unlikely explanation for the differences in helix propensity in these peptide systems.The electrostatic field resulting from the helix dipole has been proposed as yet another factor that contributes to both helix stability and specificity (64Shoemaker K.R. Kim P.S. Brems D.N. Marqusee S. York E.J. Chaiken I.M. Proc. Natl. Acad. Sci. U. S. A. 1985; 82: 2349-2353Crossref PubMed Scopus (309) Google Scholar, 65Shoemaker K.R. Kim P.S. York E.J. Stewart J.M. Baldwin R.L. Nature. 1987; 326: 563-567Crossref PubMed Scopus (569) Google Scholar). Åqvist et al. (66Åqvist J. Luecke H. Quiocho F.A. Warshel A. Proc. Natl. Acad. Sci. U. S. A. 1991; 88: 2026-2030Crossref PubMed Scopus (186) Google Scholar) demonstrated that this effect is short-ranged, and its influence is confined largely to individual backbone dipoles localized within the first and last turns of the helix, resulting in a formal positive charge at the helix N terminus and formal negative charge at the C terminus. backbone can be by side chain a fact which the early that the helix N terminus tends to be in while the C terminus is in residues D.E. M. Biopolymers. 1975; 14: PubMed Scopus (105) Google Scholar, G.D. Adv. Mol. Biol. 1978; 47: Google Scholar). These electrostatic interactions involve side hydrogen thereby the helix dipole to helix the two effects can be (39Zhukovsky E.A. Mulkerrin M.G. Presta L.G. Biochemistry. 1994; 33: 9856-9864Crossref PubMed Scopus (41) Google idea that the of side chain apolar is an important of helix stability in both proteins M. Zhang X.J. Matthews B.W. Science. 1993; 260: 1637-1640Crossref PubMed Scopus (436) Google Scholar, 56Blaber M. Zhang X.J. Lindstrom J.D. Pepiot S.D. Baase W.A. Matthews B.W. J. Mol. Biol. 1994; 235: 600-624Crossref PubMed Scopus (183) Google Scholar) and alanine-based peptides A.S. Honig B. J. Mol. Biol. 1995; 252: 351-365Crossref PubMed Scopus (225) Google Scholar). would be to the in the by these A.S. Honig B. J. Mol. Biol. 1995; 252: 351-365Crossref PubMed Scopus (225) Google Scholar, 56Blaber M. Zhang X.J. Lindstrom J.D. Pepiot S.D. Baase W.A. Matthews B.W. J. Mol. Biol. 1994; 235: 600-624Crossref PubMed Scopus (183) Google Scholar), most of the stabilization energy must be by side chain to backbone among side chains are in an alanine-based peptide because the cannot one Although interactions between side chains are possible in peptides of such interactions are too and to as a general explanation of side chains pay an entropic price that any and their net effect is to the S. Baldwin R.L. J. Mol. Biol. 1994; 241: PubMed Scopus Google Scholar, T.P. Rose G.D. Protein Sci. 1995; 4: PubMed Scopus Google hydrophobic by of side chain apolar is to the difference in between the helix and coil Although the of a residue side chain in a helix is the corresponding in the coil state is D. J. 1996; 10: PubMed Scopus Google Scholar). an extended is to the coil state, but this is to T.P. Srinivasan R. Rose G.D. Biochemistry. 1995; 34: PubMed Scopus Google Scholar). an et al. T.P. Srinivasan R. Rose G.D. Biochemistry. 1995; 34: PubMed Scopus Google Scholar) two that the expected of the coil between One was by peptides and the other by fragments from these was shown that the by apolar side chains upon helix formation is than that from a from the coil to a an alanine side chain an between and and a valine side chain an between and results our In the a central residue in a peptide is by while in the helix, that same residue would be into a a Thus, loss of side chain apolar from side interactions is an of helix the conclusions from these the α-helix is an energetically conformation for main chain specificity in the side chain, where loss of conformational entropy upon helix formation is a of the of residues in both peptides and helix capping contributes hypothesis of that the state of a of proteins to a of free energy Science. PubMed Scopus Google Scholar). that the is the protein will have all conformational entropy or Therefore, would that an to the folding is to the this is into by of the α-helix in the side chain conformational entropy is a of helix propensity in both peptides and In peptides, the some are helical and others are not is in large by differences in the entropic price that their side chains must pay to leave the coil state and adopt a helical conformation. A exists in proteins where there are only two substantially populated regions in ϕ,ψ Protein Sci. 1996; PubMed Scopus Google Scholar) that a residue can α and β, corresponding to regions of the ϕ,ψ map near (−60°,−40°) and (−120°,+135°), respectively. to β (i.e. an extended steric on the conformation of side Thus, helix propensities in proteins involve entropy differences between extended and helical conclusion from these is that side chain conformational entropy a protein will be helical or This is of central to the folding The protein is almost of residues from either or Srinivasan and G. D. Rose, a of the fact that these two secondary are in their to provide backbone with hydrogen bond partners Presta L.G. Dill K.A. Rose G.D. J. Mol. Biol. 1992; PubMed Scopus Google Scholar). In other conformational entropy is in the structure of the protein and its effect is exerted in between helix or loss of side chain conformational entropy the effect of side chain atoms into the of the chain steric factors affect and their influence is local, with other atoms close in sequence R. Rose G.D. Proteins Struct. Funct. Genet. 1995; 22: PubMed Scopus Google Scholar). For the results of two identical one of a polyalanine and the other of a similar where the central alanine has been by a The presence of even the single valine the helix by to at an steric interactions will have influence on because, in a helix, side chain and γ-carbons cannot the backbone of an helical these a simple of the folding are large to a within which hydrophobic groups can be hydrophobic side chains are to the polar backbone, which is also in most C. J. Mol. Biol. 1976; PubMed Scopus Google Scholar). this backbone to within the then hydrogen bonding would the conformational far toward the state, where backbone groups to solvent water. with this almost all backbone groups within the of proteins of known structure are found to be Presta L.G. Dill K.A. Rose G.D. J. Mol. Biol. 1992; PubMed Scopus Google Scholar). There are only two that provide hydrogen bonding for α-helix and (1Pauling L. Corey R.B. Branson H.R. Proc. Natl. Acad. Sci. U. S. A. 1951; 37: 205-210Crossref PubMed Scopus (1908) Google Scholar, L. Corey R.B. Proc. Natl. Acad. Sci. U. S. A. 1951; 37: PubMed Scopus Google Scholar). While other are found G.D. Gierasch L.M. Nature. 1983; PubMed Scopus Google Scholar), they not to hydrogen with only two conformational the C. J. Chem. Phys. 1968; Google Scholar, C. P. E. in of Scholar) is for the protein the two helix is the preferred state for the main chain, but some side chains sufficient conformational entropy in a helix that they the residue toward the only other region, extended (i.e. Thus, conformational entropy a role in between helix and that side chain conformational entropy is a must arise as an early folding within the phase of Such events will predispose residues to populate either α or β regions of ϕ,ψ Consecutive residues that populate the same become candidates for further stabilization as