Thermodynamics Of α‐Helix Formation

Advances in Protein Chemistry - Tập 72 - Trang 199-226 - 2005
George I. Makhatadze1
1¶Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033

Tài liệu tham khảo

Altmann, 1990, Helix‐coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly (hydroxybutylglutamine‐co‐L‐proline), Biopolymers, 30, 107, 10.1002/bip.360300112 Aurora, 1998, Helix capping, Protein Sci., 7, 21, 10.1002/pro.5560070103 Avbelj, 2000, Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins, J. Mol. Biol., 300, 1335, 10.1006/jmbi.2000.3901 Avbelj, 2002, Role of backbone solvation in determining thermodynamic beta propensities of the amino acids, Proc. Natl. Acad. Sci. USA, 99, 1309, 10.1073/pnas.032665499 Avbelj, 2005 Bai, 1994, Hydrogen bond strength and beta‐sheet propensities: The role of a side chain blocking effect, Proteins, 18, 262, 10.1002/prot.340180307 Baldwin, 2002, Relation between peptide backbone solvation and the energetics of peptide hydrogen bonds, Biophys. Chem., 101–102, 203, 10.1016/S0301-4622(02)00195-3 Bierzynski, 1982, A salt bridge stabilizes the helix formed by isolated C‐peptide of RNase A, Proc. Natl. Acad. Sci. USA, 79, 2470, 10.1073/pnas.79.8.2470 Blaber, 1994, Determination of alpha‐helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme, J. Mol. Biol., 235, 600, 10.1006/jmbi.1994.1016 Brooks, 2002, Protein and peptide folding explored with molecular simulations, Acc. Chem. Res., 35, 447, 10.1021/ar0100172 Brown, 1971, Helix‐coil transition of the isolated amino terminus of ribonuclease, Biochemistry, 10, 470, 10.1021/bi00779a019 Chakrabartty, 1995, Stability of alpha‐helices, Adv. Protein Chem., 46, 141, 10.1016/S0065-3233(08)60334-4 Chellgren, 2004, Effects of H2O and D2O on polyproline II helical structure, J. Am. Chem. Soc., 126, 14734, 10.1021/ja045425q Chou, 1974, Conformational parameters for amino acids in helical, beta‐sheet, and random coil regions calculated from proteins, Biochemistry, 13, 211, 10.1021/bi00699a001 Chou, 1974, Prediction of protein conformation, Biochemistry, 13, 222, 10.1021/bi00699a002 Chou, 1971, Calorimetric measurement of enthalpy change in the isothermal helix–coil transition of poly‐L‐lysine in aqueous solution, Biopolymers, 10, 657, 10.1002/bip.360100406 Cook, 1967, The relation between amino acid sequence and protein conformation, J. Mol. Biol., 29, 167, 10.1016/0022-2836(67)90188-X Creamer, 1992, Side‐chain entropy opposes alpha‐helix formation but rationalizes experimentally determined helix‐forming propensities, Proc. Natl. Acad. Sci. USA, 89, 5937, 10.1073/pnas.89.13.5937 Creamer, 1994, Alpha‐helix‐forming propensities in peptides and proteins, Proteins, 19, 85, 10.1002/prot.340190202 Daggett, 1992, Molecular dynamics simulations of helix denaturation, J. Mol. Biol., 223, 1121, 10.1016/0022-2836(92)90264-K Doig, 2002, Recent advances in helix‐coil theory, Biophys. Chem., 101–102, 281, 10.1016/S0301-4622(02)00170-9 Doig, 1994, Determination of free energies of N‐capping in alpha‐helices by modification of the Lifson‐Roig helix‐coil therapy to include N‐ and C‐capping, Biochemistry, 33, 3396, 10.1021/bi00177a033 Drozdov, 2004, Role of solvent in determining conformational preferences of alanine dipeptide in water, J. Am. Chem. Soc., 126, 2574, 10.1021/ja039051x Dygert, 1976, Helix‐coil stability constants for the naturally occurring amino acids in water. 11. Lysine parameters from random poly(hydroxybutylglutamine‐co‐L‐lysine), Macromolecules, 9, 794, 10.1021/ma60053a021 Ermolenko, 2003, Noncharged amino acid residues at the solvent‐exposed positions in the middle and at the C terminus of the alpha‐helix have the same helical propensity, Protein Sci., 12, 1169, 10.1110/ps.0304303 Ermolenko, 2002, Hydrophobic interactions at the Ccap position of the C‐capping motif of alpha‐helices, J. Mol. Biol., 322, 123, 10.1016/S0022-2836(02)00734-9 Fleming, 2005, A novel method reveals that solvent water favors polyproline II over beta‐strand conformation in peptides and unfolded proteins: Conditional hydrophobic accessible surface area (CHASA), Protein Sci., 14, 111, 10.1110/ps.041047005 Garcia, 2002, Alpha‐helical stabilization by side chain shielding of backbone hydrogen bonds, Proc. Natl. Acad. Sci. USA, 99, 2782, 10.1073/pnas.042496899 Gnanakaran, 2003, Peptide folding simulations, Curr. Opin. Struct. Biol., 13, 168, 10.1016/S0959-440X(03)00040-X Goch, 2003, Experimental investigation of initial steps of helix propagation in model peptides, Biochemistry, 42, 6840, 10.1021/bi027339d Guzzo, 1965, The influence of amino‐acid sequence on protein structure, Biophys. J., 5, 809, 10.1016/S0006-3495(65)86753-4 Gvritishvili, 2005 Hill, 1977, Helix‐coil stability constants for the naturally occurring amino acids in water. XIV. Methionine parameters from random poly(hydroxypropylglutamine, L‐methionine), Biopolymers, 16, 2447, 10.1002/bip.1977.360161109 Hiltpold, 2000, Free energy surface of the helical peptide Y(MEARA)6, J. Phys. Chem. B, 104, 10080, 10.1021/jp002207k Horovitz, 1992, Alpha‐helix stability in proteins. II. Factors that influence stability at an internal position, J. Mol. Biol., 227, 560, 10.1016/0022-2836(92)90907-2 Irback, 2005, Folding thermodynamics of peptides, Biophys. J., 88, 1560, 10.1529/biophysj.104.050427 Kendrew, 1958, A three‐dimensional model of the myoglobin molecule obtained by x‐ray analysis, Nature, 181, 662, 10.1038/181662a0 Kobayashi, 1977, Helix‐coil stability constants for the naturally occurring amino acids in water. 16. Aspartic acid parameters from random poly(hydroxybutylglutamine‐co‐L‐aspartic acid), Macromolecules, 10, 1271, 10.1021/ma60060a022 Konishi, 1977, Helix‐coil stability constants for the naturally occurring amino acids in water. 15. Arginine parameters from random poly(hydroxybutylglutamine‐co‐L‐arginine), Macromolecules, 10, 1264, 10.1021/ma60060a021 Kumar, 1996, Structural and sequence characteristics of long alpha helices in globular proteins, Biophys. J., 71, 1574, 10.1016/S0006-3495(96)79360-8 Lacroix, 1998, Elucidating the folding problem of alpha‐helices: Local motifs, long‐range electrostatics, ionic‐strength dependence and prediction of NMR parameters, J. Mol. Biol., 284, 173, 10.1006/jmbi.1998.2145 Lazaridis, 1995, Enthalpic contribution to protein stability: Insights from atom‐based calculations and statistical mechanics, Adv. Protein Chem., 47, 231, 10.1016/S0065-3233(08)60547-1 Lee, 2005, Electrostatic interactions contribute to reduced heat capacity change of unfolding in a thermophilic ribosomal protein l30e, J. Mol. Biol., 348, 419, 10.1016/j.jmb.2005.02.052 Lifson, 1961, On the theory of helix‐coil transition in polypeptides, J. Chem. Phys., 34, 1963, 10.1063/1.1731802 Loladze, 2001, Heat capacity changes upon burial of polar and nonpolar groups in proteins, Protein Sci., 10, 1343, 10.1110/ps.370101 Loladze, 2002, Thermodynamic consequences of burial of polar and non‐polar amino acid residues in the protein interior, J. Mol. Biol., 320, 343, 10.1016/S0022-2836(02)00465-5 Loladze, 2005, Both helical propensity and side‐chain hydrophobicity at a partially exposed site in alpha‐helix contribute to the thermodynamic stability of ubiquitin, Proteins, 58, 1, 10.1002/prot.20283 Lopez, 2002, The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal‐binding to induce helix formation, Proc. Natl. Acad. Sci. USA, 99, 1298, 10.1073/pnas.032665199 Luo, 1999, Interaction between water and polar groups of the helix backbone: An important determinant of helix propensities, Proc. Natl. Acad. Sci. USA, 96, 4930, 10.1073/pnas.96.9.4930 Lyu, 1990, Side chain contributions to the stability of alpha‐helical structure in peptides, Science, 250, 669, 10.1126/science.2237416 Makhatadze, 1998, Heat capacities of amino acids, peptides and proteins, Biophys. Chem., 71, 133, 10.1016/S0301-4622(98)00095-7 Makhatadze, 1990, Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: Hydration effect, J. Mol. Biol., 213, 375, 10.1016/S0022-2836(05)80197-4 Makhatadze, 1995, Energetics of protein structure, Adv. Protein Chem., 47, 307, 10.1016/S0065-3233(08)60548-3 Matheson, 1977, Helix‐coil stability constants for the naturally occurring amino acids in water. XII. Asparagine parameters from random poly(hydroxybutylglutamine‐co‐L‐asparagine), Biopolymers, 16, 1567, 10.1002/bip.1977.360160715 Maxfield, 1975, Helix‐coil stability constants for the naturally occurring amino acids in water. IX. Glutamic acid parameters from random poly(hydroxybutylglutamine‐co‐L‐glutamic acid), Macromolecules, 8, 479, 10.1021/ma60046a021 Merutka, 1990, Effect of central‐residue replacements on the helical stability of a monomeric peptide, Biochemistry, 29, 7511, 10.1021/bi00484a021 Munoz, 1994, Elucidating the folding problem of helical peptides using empirical parameters, Nat. Struct. Biol., 1, 399, 10.1038/nsb0694-399 Munoz, 1995, Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides, J. Mol. Biol., 245, 275, 10.1006/jmbi.1994.0023 Munoz, 1995, Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence, J. Mol. Biol., 245, 297, 10.1006/jmbi.1994.0024 Murphy, 1992, Thermodynamics of structural stability and cooperative folding behavior in proteins, Adv. Protein Chem., 43, 313, 10.1016/S0065-3233(08)60556-2 Myers, 1995, Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding, Protein Sci., 4, 2138, 10.1002/pro.5560041020 Myers, 1997, A direct comparison of helix propensity in proteins and peptides, Proc. Natl. Acad. Sci. USA, 94, 2833, 10.1073/pnas.94.7.2833 Myers, 1997, Helix propensities are identical in proteins and peptides, Biochemistry, 36, 10923, 10.1021/bi9707180 Nispen, 1977, Helix‐coil stability constants for the naturally occurring amino acids in water. XIII. The presence of by‐products in amino‐acid analysis of copolymers and their effect on the guest parameters; recomputed values of sigma and s for L‐serine, Biopolymers, 16, 1587, 10.1002/bip.1977.360160716 Nymeyer, 2003, Simulation of the folding equilibrium of alpha‐helical peptides: A comparison of the generalized Born approximation with explicit solvent, Proc. Natl. Acad. Sci. USA, 100, 13934, 10.1073/pnas.2232868100 Nymeyer, 2004, Atomic simulations of protein folding, using the replica exchange algorithm, Methods Enzymol., 383, 119, 10.1016/S0076-6879(04)83006-4 O'Neil, 1990, A thermodynamic scale for the helix‐forming tendencies of the commonly occurring amino acids, Science, 250, 646, 10.1126/science.2237415 Pace, 1998, A helix propensity scale based on experimental studies of peptides and proteins, Biophys. J., 75, 422, 10.1016/S0006-3495(98)77529-0 Padmanabhan, 1990, Relative helix‐forming tendencies of nonpolar amino acids, Nature, 344, 268, 10.1038/344268a0 Paschek, 2005, Chemical theory and computation special feature: Simulations of the pressure and temperature unfolding of an alpha‐helical peptide, Proc. Natl. Acad. Sci. USA, 102, 6765, 10.1073/pnas.0408527102 Pauling, 1951, The structures of proteins: Two hydrogen bonded helical configurations of polypeptide chain, Proc. Natl. Acad. Sci. USA, 37, 205, 10.1073/pnas.37.4.205 Penel, 1999, Side‐chain structures in the first turn of the alpha‐helix, J. Mol. Biol., 287, 127, 10.1006/jmbi.1998.2549 Prothero, 1966, Correlation between the distribution of amino acids and alpha helices, Biophys. J., 6, 367, 10.1016/S0006-3495(66)86662-6 Ptitsyn, 1969, Statistical analysis of the distribution of amino acid residues among helical and non‐helical regions in globular proteins, J. Mol. Biol., 42, 501, 10.1016/0022-2836(69)90238-1 Rialdi, 1966, Calorimetric heat of the helix‐coil transition of poly‐L‐glutamic acid, J. Am. Chem. Soc., 88, 5719, 10.1021/ja00976a007 Richardson, 2005, Enthalpy of helix‐coil transition: Missing link in rationalizing the thermodynamics of helix‐forming propensities of the amino acid residues, Proc. Natl. Acad. Sci. USA, 102, 1413, 10.1073/pnas.0408004102 Richardson, 2004, Temperature dependence of the thermodynamics of helix‐coil transition, J. Mol. Biol., 335, 1029, 10.1016/j.jmb.2003.11.027 Richardson, 1999, MEARA sequence repeat of human CstF‐64 polyadenylation factor is helical in solution: A spectroscopic and calorimetric study, Biochemistry, 38, 12869, 10.1021/bi990724r Rohl, 1998, Deciphering rules of helix stability in peptides, Methods Enzymol., 295, 1, 10.1016/S0076-6879(98)95032-7 Rohl, 1996, Helix propagation and N‐cap propensities of the amino acids measured in alanine‐based peptides in 40 volume percent trifluoroethanol, Protein Sci., 5, 2623, 10.1002/pro.5560051225 Rohl, 1996, Models for the 3(10)‐helix/coil, pi‐helix/coil, and alpha‐helix/3(10)‐helix/coil transitions in isolated peptides, Protein Sci., 5, 1687, 10.1002/pro.5560050822 Rohl, 1999, Alanine is helix‐stabilizing in both template‐nucleated and standard peptide helices, Proc. Natl. Acad. Sci. USA, 96, 3682, 10.1073/pnas.96.7.3682 Schellman, 1955, The stability of hydrogen‐bonded peptide structures in aqueous solution, C. R. Trav. Lab. Carlsberg Ser. Chim., 29, 230 Schellman, 1955, The thermodynamics of urea solutions and the heat of formation of the peptide hydrogen bond, C. R. Trav. Lab. Carlsberg Ser. Chim., 29, 223 Schellman, 1992, Helix‐coil theories: A comparative study for finite length polypeptides, J. Phys. Chem., 96, 3987, 10.1021/j100189a015 Scheule, 1976, Helix–coil stability constants for the naturally occurring amino acids in water. X. Tyrosine parameters from random poly(hydroxypropylglutamine‐co‐L‐tyrosine), Macromolecules, 9, 23, 10.1021/ma60049a005 Scholtz, 1992, The mechanism of alpha‐helix formation by peptides, Annu. Rev. Biophys. Biomol. Struct., 21, 95, 10.1146/annurev.bb.21.060192.000523 Scholtz, 1991, Calorimetric determination of the enthalpy change for the alpha‐helix to coil transition of an alanine peptide in water, Proc. Natl. Acad. Sci. USA, 88, 2854, 10.1073/pnas.88.7.2854 Scholtz, 1991, Parameters of helix‐coil transition theory for alanine‐based peptides of varying chain lengths in water, Biopolymers, 31, 1463, 10.1002/bip.360311304 Seale, 1994, Sequence determinants of the capping box, a stabilizing motif at the N‐termini of alpha‐helices, Protein Sci., 3, 1741, 10.1002/pro.5560031014 Serrano, 1992, Alpha‐helix stability in proteins. I. Empirical correlations concerning substitution of side‐chains at the N and C‐caps and the replacement of alanine by glycine or serine at solvent‐exposed surfaces, J. Mol. Biol., 227, 544, 10.1016/0022-2836(92)90906-Z Shental‐Bechor, 2005, Monte Carlo studies of folding, dynamics, and stability in alpha‐helices, Biophys. J., 88, 2391, 10.1529/biophysj.104.050708 Siedlecka, 1999, Alpha‐helix nucleation by a calcium‐binding peptide loop, Proc. Natl. Acad. Sci. USA, 96, 903, 10.1073/pnas.96.3.903 Snow, 2005, How well can simulation predict protein folding kinetics and thermodynamics?, Annu. Rev. Biophys. Biomol. Struct., 34, 43, 10.1146/annurev.biophys.34.040204.144447 Sorin, 2005, Exploring the helix‐coil transition via all‐atom equilibrium ensemble simulations, Biophys. J., 88, 2472, 10.1529/biophysj.104.051938 Spolar, 1992, Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water, Biochemistry, 31, 3947, 10.1021/bi00131a009 Stapley, 1995, Addition of side chain interactions to modified Lifson–Roig helix‐coil theory: Application to energetics of phenylalanine–methionine interactions, Protein Sci., 4, 2383, 10.1002/pro.5560041117 Sueki, 1984, Helix‐coil stability constants for the naturally occurring amino acids in water. 22. Histidine parameters from random poly[(hydroxybutyl)glutamine‐co‐L‐histidine], Macromolecules, 17, 148, 10.1021/ma00132a006 Thomas, 2001, Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C′ position of the C‐capping box of alpha‐helices, Proc. Natl. Acad. Sci. USA, 98, 10670, 10.1073/pnas.191381798 Thomas, 2000, Contribution of the 30/36 hydrophobic contact at the C‐terminus of the alpha‐helix to the stability of the ubiquitin molecule, Biochemistry, 39, 10275, 10.1021/bi0000418 Van Wart, 1973, Helix‐coil stability constants for the naturally occurring amino acids in water. VII. Phenylalanine parameters from random poly(hydroxypropylglutamine‐co‐L‐phenylalanine), Macromolecules, 6, 266, 10.1021/ma60032a025 Wieprecht, 1999, Thermodynamics of the alpha‐helix‐coil transition of amphipathic peptides in a membrane environment: Implications for the peptide‐membrane binding equilibrium, J. Mol. Biol., 294, 785, 10.1006/jmbi.1999.3268 Wojcik, 1990, Helix‐coil stability constants for the naturally occurring amino acids in water. XXIV. Half‐cystine parameters from random poly(hydroxybutylglutamine‐co‐S‐methylthio‐L‐cysteine), Biopolymers, 30, 121, 10.1002/bip.360300113 Wojcik, 1997, Isolated calcium‐binding loops of EF‐hand proteins can dimerize to form a native‐like structure, Biochemistry, 36, 680, 10.1021/bi961821c Yang, 1995, Free energy determinants of secondary structure formation. I. alpha‐helices, J. Mol. Biol., 252, 351, 10.1006/jmbi.1995.0502 Young, 1996, A microscopic view of helix propagation: N and C‐terminal helix growth in alanine helices, J. Mol. Biol., 259, 560, 10.1006/jmbi.1996.0339 Zhou, 2002, Toward the physical basis of thermophilic proteins: Linking of enriched polar interactions and reduced heat capacity of unfolding, Biophys. J., 83, 3126, 10.1016/S0006-3495(02)75316-2 Zimm, 1959, Theory of the phase transition between helix and random coil in polypeptide chains, J. Chem. Phys., 31, 526, 10.1063/1.1730390