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Design of Stable Alpha-helices Using Global Sequence Optimization

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Springer Protocols

De Novo Design of Stable α-Helices

Authors:

Alexander Yakimov 1 , 2 ,

Georgy Rychkov 1 , 2 ,

Michael Petukhov Author Email 1 , 2

Alexander Yakimov 1 , 2 ,

Georgy Rychkov 1 , 2 ,

Michael Petukhov Author Email 1 , 2

Series: Methods In Molecular Biology > Book: Protein Design

Protocol | DOI: 10.1007/978-1-4939-1486-9_1

Affiliations:

  1. Saint Petersburg State Polytechnical University, Saint Petersburg, Russia
  2. Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia

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Abstract

Recent studies have elucidated key principles governing folding and stability of α-helices in short peptides and globular proteins. In this chapter we review briefly those principles and describe a protocol for the de novo design of highly stable

…more

Recent studies have elucidated key principles governing folding and stability of α-helices in short peptides and globular proteins. In this chapter we review briefly those principles and describe a protocol for the de novo design of highly stable α-helixes using the SEQOPT algorithm. This algorithm is based on AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides, and the tunneling algorithm for global sequence optimization.

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Figures (0) & Videos (0)

Keywords

Techniques:

Conjugate Gradient Method, Molecular Modeling, Molecular Dynamics Simulation, Circular Dichroism, NMR, Structure Determination

Others:

Stability, Solubility, α-Helix, Sequence optimization

Citations (6)

Related articles

References

  1. Estieu-Gionnet K, Guichard G (2011) Stabilized helical peptides: overview of the technologies and therapeutic promises. Expert Opin Drug Discov 6:937–963
  2. Finkelstein AV, Badretdinov AY, Ptitsyn OB (1991) Physical reasons for secondary structure stability: alpha-helices in short peptides. Proteins 10:287–299
  3. Scholtz JM, Baldwin RL (1992) The mechanism of alpha-helix formation by peptides. Annu Rev Biophys Biomol Struct 21:95–118
  4. Errington N, Iqbalsyah T, Doig AJ (2006) Structure and stability of the alpha-helix: lessons for design. Methods Mol Biol 340:3–26
  5. Petukhov M, Tatsu Y, Tamaki K, Murase S, Uekawa H, Yoshikawa S et al (2009) Design of stable alpha-helices using global sequence optimization. J Pept Sci 15:359–365
  6. Azzarito V, Long K, Murphy NS, Wilson AJ (2013) Inhibition of [alpha]-helix-mediated protein-protein interactions using designed molecules. Nat Chem 5:161–173
  7. Armstrong KM, Fairman R, Baldwin RL (1993) The (i, i + 4) Phe-His interaction studied in an alanine-based alpha-helix. J Mol Biol 230:284–291
  8. Huyghues-Despointes BM, Scholtz JM, Baldwin RL (1993) Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings. Protein Sci 2:80–85
  9. Padmanabhan S, Baldwin RL (1994) Tests for helix-stabilizing interactions between various nonpolar side chains in alanine-based peptides. Protein Sci 3:1992–1997
  10. Lockhart DJ, Kim PS (1992) Internal stark effect measurement of the electric field at the amino terminus of an alpha helix. Science 257:947–951
  11. Aurora R, Rose GD (1998) Helix capping. Protein Sci 7:21–38
  12. Bryson JW, Betz SF, Lu HS, Suich DJ, Zhou HX, O'Neil KT et al (1995) Protein design: a hierarchic approach. Science 270:935–941
  13. Villegas V, Viguera AR, Avilés FX, Serrano L (1996) Stabilization of proteins by rational design of alpha-helix stability using helix/coil transition theory. Fold Des 1:29–34
  14. Liu Y, Kuhlman B (2006) RosettaDesign server for protein design. Nucleic Acids Res 34(Web Server):W235–W238
  15. Pokala N, Handel TM (2004) Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation. Protein Sci 13:925–936
  16. Liang S, Grishin NV (2003) Effective scoring function for protein sequence design. Proteins 54:271–281
  17. Dai L, Yang Y, Kim HR, Zhou Y (2010) Improving computational protein design by using structure-derived sequence profile. Proteins 78:2338–2348
  18. Li Z, Yang Y, Zhan J, Dai L, Zhou Y (2013) Energy functions in de novo protein design: current challenges and future prospects. Annu Rev Biophys 42:315–335
  19. Levy A, Montalvo A (1985) The tunneling algorithm for the global minimization of functions. SIAM J Sci Comput 6:15–29
  20. Muñoz V, Serrano L (1994) Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol 1:399–409
  21. Muñoz V, Serrano L (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 245:275–296
  22. Muñoz V, Serrano L (1995) Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence. J Mol Biol 245:297–308
  23. Petukhov M, Yumoto N, Murase S, Onmura R, Yoshikawa S (1996) Factors that affect the stabilization of alpha-helices in short peptides by a capping box. Biochemistry 35:387–397
  24. Lacroix E, Viguera AR, Serrano L (1998) Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 284:173–191
  25. Petukhov M, Muñoz V, Yumoto N, Yoshikawa S, Serrano L (1998) Position dependence of non-polar amino acid intrinsic helical propensities. J Mol Biol 278:279–289
  26. Petukhov M, Uegaki K, Yumoto N, Yoshikawa S, Serrano L (1999) Position dependence of amino acid intrinsic helical propensities II: non-charged polar residues: Ser, Thr, Asn, and Gln. Protein Sci 8:2144–2150
  27. Petukhov M, Uegaki K, Yumoto N, Serrano L (2002) Amino acid intrinsic alpha-helical propensities III: positional dependence at several positions of C terminus. Protein Sci 11:766–777
  28. Muñoz V, Serrano L (1997) Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers 41:495–509
  29. Finkelstein AV, Ptitsyn OB (1976) A theory of protein molecule self-organization. IV. Helical and irregular local structures of unfolded protein chains. J Mol Biol 103:15–24
  30. Finkelstein AV (1977) Theory of protein molecule self-organization. III. A calculating method for the probabilities of the secondary structure formation in an unfolded polypeptide chain. Biopolymers 16:525–529
  31. Finkelstein AV (1977) Electrostatic interactions of charged groups in water environment and their influence on the polypeptide chain secondary structure formation. Molek Biol (USSR) 10:811–819
  32. Finkelstein AV, Ptitsyn OB (1977) Theory of protein molecule self-organization. I. Thermodynamic parameters of local secondary structures in the unfolded protein chain. Biopolymers 16:469–495
  33. Finkelstein AV, Ptitsyn OB, Kozitsyn SA (1977) Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments. Biopolymers 16:497–524
  34. Bierzynski A, Kim PS, Baldwin RL (1982) A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A. Proc Natl Acad Sci U S A 79:2470–2474
  35. Kim PS, Baldwin RL (1984) A helix stop signal in the isolated S-peptide of ribonuclease A. Nature 307:329–334
  36. Creamer TP, Rose GD (1994) Alpha-helix-forming propensities in peptides and proteins. Proteins 19:85–97
  37. Avbelj F, Moult J (1995) Role of electrostatic screening in determining protein main chain conformational preferences. Biochemistry 34:755–764
  38. Chang DK, Cheng SF, Trivedi VD, Lin KL (1999) Proline affects oligomerization of a coiled coil by inducing a kink in a long helix. J Struct Biol 128:270–279
  39. Viguera AR, Serrano L (1999) Stable proline box motif at the N-terminal end of alpha-helices. Protein Sci 8:1733–1742
  40. Strehlow KG, Baldwin RL (1989) Effect of the substitution Ala––Gly at each of five residue positions in the C-peptide helix. Biochemistry 28:2130–2133
  41. Stapley BJ, Rohl CA, Doig AJ (1995) Addition of side chain interactions to modified Lifson-Roig helix-coil theory: application to energetics of phenylalanine-methionine interactions. Protein Sci 4:2383–2391
  42. Seale JW, Srinivasan R, Rose GD (1994) Sequence determinants of the capping box, a stabilizing motif at the N-termini of α-helices. Protein Sci 3:1741–1745
  43. Muñoz V, Blanco FJ, Serrano L (1995) The hydrophobic-staple motif and a role for loop-residues in alpha-helix stability and protein folding. Nat Struct Biol 2:380–385
  44. Aurora R, Srinivasan R, Rose GD (1994) Rules for alpha-helix termination by glycine. Science 264:1126–1130
  45. Viguera AR, Serrano L (1995) Experimental analysis of the Schellman motif. J Mol Biol 251:150–160
  46. Zimm BH, Doty P, Iso K (1959) Determination of the parameters for helix formation in poly-gamma-benzyl-l-glutamate. Proc Natl Acad Sci U S A 45:1601–1607
  47. Lifson S, Roig A (1961) On the theory of helix—coil transition in polypeptides. J Chem Phys 34:1963–1973
  48. Harper ET, Rose GD (1993) Helix stop signals in proteins and peptides: the capping box. Biochemistry 32(30):7605–7609
  49. Himmelblau DM (1972) Applied nonlinear programming. McGraw-Hill, New York
  50. Bartenev OV (2000) FORTRAN for professionals 1. Dialog-MIPI, Moscow
  51. Yakimov A, Rychkov G, Petukhov M (2013) SeqOPT: web based server for rational design of conformationally stable alpha-helices in monomeric peptides and globular proteins. FEBS J 280(Suppl s1):127–128
  52. Rose GD, Wolfenden R (1993) Hydrogen bonding, hydrophobicity, packing, and protein folding. Annu Rev Biophys Biomol Struct 22:381–415
  53. Eisenberg D, Weiss RM, Terwilliger TC (1984) The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A 81:140–144
  54. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132
  55. Biswas KM, DeVido DR, Dorsey JG (2003) Evaluation of methods for measuring amino acid hydrophobicities and interactions. J Chromatogr A 1000:637–655
  56. Engelman DM, Steitz TA, Goldman A (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem 15:321–353
  57. Surzhik MA, Churkina SV, Shmidt AE, Shvetsov AV, Kozhina TN, Firsov DL, Firsov LM, Petukhov MG (2010) The effect of point amino acid substitutions in an internal alpha-helix on thermostability of Aspergillus awamori X100 glucoamylase. Prikl Biokhim Mikrobiol 46:221–227
  58. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637
  59. Abagyan R, Totrov M, Kuznetsov D (1994) ICM-A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15:488–506
  60. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688
  61. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447
  62. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98:10037–10041
  63. Best RB, de Sancho D, Mittal J (2012) Residue-specific α-helix propensities from molecular simulation. Biophys J 102:1462–1467
  64. Galzitskaya OV, Higo J, Finkelstein AV (2002) alpha-Helix and beta-hairpin folding from experiment, analytical theory and molecular dynamics simulations. Curr Protein Pept Sci 3:191–200
  65. Dodero VI, Quirolo ZB, Sequeira MA (2011) Biomolecular studies by circular dichroism. Front Biosci 16:61–73
  66. Kuwajima K (1995) Circular dichroism. Methods Mol Biol 40:115–136
  67. Chen Y-H, Yang JT (1971) A new approach to the calculation of secondary structures of globular proteins by optical rotatory dispersion and circular dichroism. Biochem Biophys Res Commun 44:1285–1291
  68. Luo P, Baldwin RL (1997) Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water. Biochemistry 36:8413–8421
  69. Hinds MG, Norton RS (1995) NMR spectroscopy of peptides and proteins. Methods Mol Biol 36:131–154

Abstract

Recent studies have elucidated key principles governing folding and stability of α-helices in short peptides and globular proteins. In this chapter we review briefly those principles and describe a protocol for the de novo design of highly stable

…more

Recent studies have elucidated key principles governing folding and stability of α-helices in short peptides and globular proteins. In this chapter we review briefly those principles and describe a protocol for the de novo design of highly stable α-helixes using the SEQOPT algorithm. This algorithm is based on AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides, and the tunneling algorithm for global sequence optimization.

less

Related articles

References

  1. Estieu-Gionnet K, Guichard G (2011) Stabilized helical peptides: overview of the technologies and therapeutic promises. Expert Opin Drug Discov 6:937–963
  2. Finkelstein AV, Badretdinov AY, Ptitsyn OB (1991) Physical reasons for secondary structure stability: alpha-helices in short peptides. Proteins 10:287–299
  3. Scholtz JM, Baldwin RL (1992) The mechanism of alpha-helix formation by peptides. Annu Rev Biophys Biomol Struct 21:95–118
  4. Errington N, Iqbalsyah T, Doig AJ (2006) Structure and stability of the alpha-helix: lessons for design. Methods Mol Biol 340:3–26
  5. Petukhov M, Tatsu Y, Tamaki K, Murase S, Uekawa H, Yoshikawa S et al (2009) Design of stable alpha-helices using global sequence optimization. J Pept Sci 15:359–365
  6. Azzarito V, Long K, Murphy NS, Wilson AJ (2013) Inhibition of [alpha]-helix-mediated protein-protein interactions using designed molecules. Nat Chem 5:161–173
  7. Armstrong KM, Fairman R, Baldwin RL (1993) The (i, i + 4) Phe-His interaction studied in an alanine-based alpha-helix. J Mol Biol 230:284–291
  8. Huyghues-Despointes BM, Scholtz JM, Baldwin RL (1993) Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings. Protein Sci 2:80–85
  9. Padmanabhan S, Baldwin RL (1994) Tests for helix-stabilizing interactions between various nonpolar side chains in alanine-based peptides. Protein Sci 3:1992–1997
  10. Lockhart DJ, Kim PS (1992) Internal stark effect measurement of the electric field at the amino terminus of an alpha helix. Science 257:947–951
  11. Aurora R, Rose GD (1998) Helix capping. Protein Sci 7:21–38
  12. Bryson JW, Betz SF, Lu HS, Suich DJ, Zhou HX, O'Neil KT et al (1995) Protein design: a hierarchic approach. Science 270:935–941
  13. Villegas V, Viguera AR, Avilés FX, Serrano L (1996) Stabilization of proteins by rational design of alpha-helix stability using helix/coil transition theory. Fold Des 1:29–34
  14. Liu Y, Kuhlman B (2006) RosettaDesign server for protein design. Nucleic Acids Res 34(Web Server):W235–W238
  15. Pokala N, Handel TM (2004) Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation. Protein Sci 13:925–936
  16. Liang S, Grishin NV (2003) Effective scoring function for protein sequence design. Proteins 54:271–281
  17. Dai L, Yang Y, Kim HR, Zhou Y (2010) Improving computational protein design by using structure-derived sequence profile. Proteins 78:2338–2348
  18. Li Z, Yang Y, Zhan J, Dai L, Zhou Y (2013) Energy functions in de novo protein design: current challenges and future prospects. Annu Rev Biophys 42:315–335
  19. Levy A, Montalvo A (1985) The tunneling algorithm for the global minimization of functions. SIAM J Sci Comput 6:15–29
  20. Muñoz V, Serrano L (1994) Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol 1:399–409
  21. Muñoz V, Serrano L (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 245:275–296
  22. Muñoz V, Serrano L (1995) Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence. J Mol Biol 245:297–308
  23. Petukhov M, Yumoto N, Murase S, Onmura R, Yoshikawa S (1996) Factors that affect the stabilization of alpha-helices in short peptides by a capping box. Biochemistry 35:387–397
  24. Lacroix E, Viguera AR, Serrano L (1998) Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 284:173–191
  25. Petukhov M, Muñoz V, Yumoto N, Yoshikawa S, Serrano L (1998) Position dependence of non-polar amino acid intrinsic helical propensities. J Mol Biol 278:279–289
  26. Petukhov M, Uegaki K, Yumoto N, Yoshikawa S, Serrano L (1999) Position dependence of amino acid intrinsic helical propensities II: non-charged polar residues: Ser, Thr, Asn, and Gln. Protein Sci 8:2144–2150
  27. Petukhov M, Uegaki K, Yumoto N, Serrano L (2002) Amino acid intrinsic alpha-helical propensities III: positional dependence at several positions of C terminus. Protein Sci 11:766–777
  28. Muñoz V, Serrano L (1997) Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers 41:495–509
  29. Finkelstein AV, Ptitsyn OB (1976) A theory of protein molecule self-organization. IV. Helical and irregular local structures of unfolded protein chains. J Mol Biol 103:15–24
  30. Finkelstein AV (1977) Theory of protein molecule self-organization. III. A calculating method for the probabilities of the secondary structure formation in an unfolded polypeptide chain. Biopolymers 16:525–529
  31. Finkelstein AV (1977) Electrostatic interactions of charged groups in water environment and their influence on the polypeptide chain secondary structure formation. Molek Biol (USSR) 10:811–819
  32. Finkelstein AV, Ptitsyn OB (1977) Theory of protein molecule self-organization. I. Thermodynamic parameters of local secondary structures in the unfolded protein chain. Biopolymers 16:469–495
  33. Finkelstein AV, Ptitsyn OB, Kozitsyn SA (1977) Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments. Biopolymers 16:497–524
  34. Bierzynski A, Kim PS, Baldwin RL (1982) A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A. Proc Natl Acad Sci U S A 79:2470–2474
  35. Kim PS, Baldwin RL (1984) A helix stop signal in the isolated S-peptide of ribonuclease A. Nature 307:329–334
  36. Creamer TP, Rose GD (1994) Alpha-helix-forming propensities in peptides and proteins. Proteins 19:85–97
  37. Avbelj F, Moult J (1995) Role of electrostatic screening in determining protein main chain conformational preferences. Biochemistry 34:755–764
  38. Chang DK, Cheng SF, Trivedi VD, Lin KL (1999) Proline affects oligomerization of a coiled coil by inducing a kink in a long helix. J Struct Biol 128:270–279
  39. Viguera AR, Serrano L (1999) Stable proline box motif at the N-terminal end of alpha-helices. Protein Sci 8:1733–1742
  40. Strehlow KG, Baldwin RL (1989) Effect of the substitution Ala––Gly at each of five residue positions in the C-peptide helix. Biochemistry 28:2130–2133
  41. Stapley BJ, Rohl CA, Doig AJ (1995) Addition of side chain interactions to modified Lifson-Roig helix-coil theory: application to energetics of phenylalanine-methionine interactions. Protein Sci 4:2383–2391
  42. Seale JW, Srinivasan R, Rose GD (1994) Sequence determinants of the capping box, a stabilizing motif at the N-termini of α-helices. Protein Sci 3:1741–1745
  43. Muñoz V, Blanco FJ, Serrano L (1995) The hydrophobic-staple motif and a role for loop-residues in alpha-helix stability and protein folding. Nat Struct Biol 2:380–385
  44. Aurora R, Srinivasan R, Rose GD (1994) Rules for alpha-helix termination by glycine. Science 264:1126–1130
  45. Viguera AR, Serrano L (1995) Experimental analysis of the Schellman motif. J Mol Biol 251:150–160
  46. Zimm BH, Doty P, Iso K (1959) Determination of the parameters for helix formation in poly-gamma-benzyl-l-glutamate. Proc Natl Acad Sci U S A 45:1601–1607
  47. Lifson S, Roig A (1961) On the theory of helix—coil transition in polypeptides. J Chem Phys 34:1963–1973
  48. Harper ET, Rose GD (1993) Helix stop signals in proteins and peptides: the capping box. Biochemistry 32(30):7605–7609
  49. Himmelblau DM (1972) Applied nonlinear programming. McGraw-Hill, New York
  50. Bartenev OV (2000) FORTRAN for professionals 1. Dialog-MIPI, Moscow
  51. Yakimov A, Rychkov G, Petukhov M (2013) SeqOPT: web based server for rational design of conformationally stable alpha-helices in monomeric peptides and globular proteins. FEBS J 280(Suppl s1):127–128
  52. Rose GD, Wolfenden R (1993) Hydrogen bonding, hydrophobicity, packing, and protein folding. Annu Rev Biophys Biomol Struct 22:381–415
  53. Eisenberg D, Weiss RM, Terwilliger TC (1984) The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A 81:140–144
  54. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132
  55. Biswas KM, DeVido DR, Dorsey JG (2003) Evaluation of methods for measuring amino acid hydrophobicities and interactions. J Chromatogr A 1000:637–655
  56. Engelman DM, Steitz TA, Goldman A (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem 15:321–353
  57. Surzhik MA, Churkina SV, Shmidt AE, Shvetsov AV, Kozhina TN, Firsov DL, Firsov LM, Petukhov MG (2010) The effect of point amino acid substitutions in an internal alpha-helix on thermostability of Aspergillus awamori X100 glucoamylase. Prikl Biokhim Mikrobiol 46:221–227
  58. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637
  59. Abagyan R, Totrov M, Kuznetsov D (1994) ICM-A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15:488–506
  60. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688
  61. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447
  62. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98:10037–10041
  63. Best RB, de Sancho D, Mittal J (2012) Residue-specific α-helix propensities from molecular simulation. Biophys J 102:1462–1467
  64. Galzitskaya OV, Higo J, Finkelstein AV (2002) alpha-Helix and beta-hairpin folding from experiment, analytical theory and molecular dynamics simulations. Curr Protein Pept Sci 3:191–200
  65. Dodero VI, Quirolo ZB, Sequeira MA (2011) Biomolecular studies by circular dichroism. Front Biosci 16:61–73
  66. Kuwajima K (1995) Circular dichroism. Methods Mol Biol 40:115–136
  67. Chen Y-H, Yang JT (1971) A new approach to the calculation of secondary structures of globular proteins by optical rotatory dispersion and circular dichroism. Biochem Biophys Res Commun 44:1285–1291
  68. Luo P, Baldwin RL (1997) Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water. Biochemistry 36:8413–8421
  69. Hinds MG, Norton RS (1995) NMR spectroscopy of peptides and proteins. Methods Mol Biol 36:131–154

Figures (0) & Videos (0)

Citations (6)

Keywords

Techniques:

Conjugate Gradient Method, Molecular Modeling, Molecular Dynamics Simulation, Circular Dichroism, NMR, Structure Determination

Others:

Stability, Solubility, α-Helix, Sequence optimization

Design of Stable Alpha-helices Using Global Sequence Optimization

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