Thermodynamics Of α‐Helix Formation
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