메뉴 건너뛰기




Volumn 117, Issue 17, 2013, Pages 4956-4964

A rapid, ensemble and free energy based method for engineering protein stabilities

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; STABILITY;

EID: 84877042928     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp401588x     Document Type: Article
Times cited : (28)

References (52)
  • 1
    • 0033584889 scopus 로고    scopus 로고
    • Selection for Improved Protein Stability by Phage Display
    • Jung, S.; Honegger, A.; Pluckthun, A. Selection for Improved Protein Stability by Phage Display J. Mol. Biol. 1999, 294, 163-180
    • (1999) J. Mol. Biol. , vol.294 , pp. 163-180
    • Jung, S.1    Honegger, A.2    Pluckthun, A.3
  • 4
    • 0000159569 scopus 로고    scopus 로고
    • Protein Structure and the Energetics of Protein Stability
    • Robertson, A. D.; Murphy, K. P. Protein Structure and the Energetics of Protein Stability Chem. Rev. 1997, 97, 1251-1267
    • (1997) Chem. Rev. , vol.97 , pp. 1251-1267
    • Robertson, A.D.1    Murphy, K.P.2
  • 5
    • 34447297323 scopus 로고    scopus 로고
    • Energetics of Protein Folding
    • Baldwin, R. L. Energetics of Protein Folding J. Mol. Biol. 2007, 371, 283-301
    • (2007) J. Mol. Biol. , vol.371 , pp. 283-301
    • Baldwin, R.L.1
  • 9
    • 2042473511 scopus 로고
    • Statistical Mechanical Theory of Protein Conformation 0.1. General Considerations and Application to Homopolymers
    • Wako, H.; Saito, N. Statistical Mechanical Theory of Protein Conformation 0.1. General Considerations and Application to Homopolymers J. Phys. Soc. Jpn. 1978, 44, 1931-1938
    • (1978) J. Phys. Soc. Jpn. , vol.44 , pp. 1931-1938
    • Wako, H.1    Saito, N.2
  • 10
    • 2042474146 scopus 로고
    • Statistical Mechanical Theory of Protein Conformation 0.2. Folding Pathway for Protein
    • Wako, H.; Saito, N. Statistical Mechanical Theory of Protein Conformation 0.2. Folding Pathway for Protein J. Phys. Soc. Jpn. 1978, 44, 1939-1945
    • (1978) J. Phys. Soc. Jpn. , vol.44 , pp. 1939-1945
    • Wako, H.1    Saito, N.2
  • 11
    • 0033613165 scopus 로고    scopus 로고
    • A Simple Model for Calculating the Kinetics of Protein Folding from Three-Dimensional Structures
    • Muñoz, V.; Eaton, W. A. A Simple Model for Calculating the Kinetics of Protein Folding from Three-Dimensional Structures Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11311-11316
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 11311-11316
    • Muñoz, V.1    Eaton, W.A.2
  • 12
    • 0035312345 scopus 로고    scopus 로고
    • What Can We Learn about Protein Folding from Ising-Like Models?
    • Muñoz, V. What Can We Learn About Protein Folding from Ising-Like Models? Curr. Opin. Struct. Biol. 2001, 11, 212-216
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 212-216
    • Muñoz, V.1
  • 15
    • 79953684009 scopus 로고    scopus 로고
    • Quantitative Prediction of Protein Folding Behaviors from a Simple Statistical Model
    • Bruscolini, P.; Naganathan, A. N. Quantitative Prediction of Protein Folding Behaviors from a Simple Statistical Model J. Am. Chem. Soc. 2011, 133, 5372-5379
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 5372-5379
    • Bruscolini, P.1    Naganathan, A.N.2
  • 16
    • 34147147538 scopus 로고    scopus 로고
    • Ising-Like Model for Protein Mechanical Unfolding
    • Imparato, A.; Pelizzola, A.; Zamparo, M. Ising-Like Model for Protein Mechanical Unfolding Phys. Rev. Lett. 2007, 98, 148102
    • (2007) Phys. Rev. Lett. , vol.98 , pp. 148102
    • Imparato, A.1    Pelizzola, A.2    Zamparo, M.3
  • 17
    • 79951900584 scopus 로고    scopus 로고
    • Analysis of the Equilibrium and Kinetics of the Ankyrin Repeat Protein Myotrophin
    • Faccin, M.; Bruscolini, P.; Pelizzola, A. Analysis of the Equilibrium and Kinetics of the Ankyrin Repeat Protein Myotrophin J. Chem. Phys. 2011, 134, 075102
    • (2011) J. Chem. Phys. , vol.134 , pp. 075102
    • Faccin, M.1    Bruscolini, P.2    Pelizzola, A.3
  • 18
    • 84856948690 scopus 로고    scopus 로고
    • Effects of Confinement on Thermal Stability and Folding Kinetics in a Simple Ising-Like Model
    • Caraglio, M.; Pelizzola, A. Effects of Confinement on Thermal Stability and Folding Kinetics in a Simple Ising-Like Model Phys. Biol. 2012, 9, 016006
    • (2012) Phys. Biol. , vol.9 , pp. 016006
    • Caraglio, M.1    Pelizzola, A.2
  • 19
    • 84869068671 scopus 로고    scopus 로고
    • Predictions from an Ising-Like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics
    • Naganathan, A. N. Predictions from an Ising-Like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics J. Chem. Theory Comput. 2012, 8, 4646-4656
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 4646-4656
    • Naganathan, A.N.1
  • 20
    • 0347123330 scopus 로고    scopus 로고
    • Thermal Denaturation and Folding Rates of Single Domain Proteins: Size Matters
    • Li, M. S.; Klimov, D. K.; Thirumalai, D. Thermal Denaturation and Folding Rates of Single Domain Proteins: Size Matters Polymer 2004, 45, 573-579
    • (2004) Polymer , vol.45 , pp. 573-579
    • Li, M.S.1    Klimov, D.K.2    Thirumalai, D.3
  • 21
    • 12944309313 scopus 로고    scopus 로고
    • Scaling of Folding Times with Protein Size
    • Naganathan, A. N.; Muñoz, V. Scaling of Folding Times with Protein Size J. Am. Chem. Soc. 2005, 127, 480-481
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 480-481
    • Naganathan, A.N.1    Muñoz, V.2
  • 22
    • 8644232696 scopus 로고    scopus 로고
    • Combinatorial Modeling of Protein Folding Kinetics: Free Energy Profiles and Rates
    • Henry, E. R.; Eaton, W. A. Combinatorial Modeling of Protein Folding Kinetics: Free Energy Profiles and Rates Chem. Phys. 2004, 307, 163-185
    • (2004) Chem. Phys. , vol.307 , pp. 163-185
    • Henry, E.R.1    Eaton, W.A.2
  • 23
    • 0032502839 scopus 로고    scopus 로고
    • Contact Order, Transition State Placement and the Refolding Rates of Single Domain Proteins
    • Plaxco, K. W.; Simons, K. T.; Baker, D. Contact Order, Transition State Placement and the Refolding Rates of Single Domain Proteins J. Mol. Biol. 1998, 227, 985-994
    • (1998) J. Mol. Biol. , vol.227 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 24
    • 0035967862 scopus 로고    scopus 로고
    • Comparison between Long-Range Interactions and Contact Order in Determining the Folding Rate of Two-State Proteins: Application of Long-Range Order to Folding Rate Prediction
    • Gromiha, M. M.; Selvaraj, S. Comparison between Long-Range Interactions and Contact Order in Determining the Folding Rate of Two-State Proteins: Application of Long-Range Order to Folding Rate Prediction J. Mol. Biol. 2001, 310, 27-32
    • (2001) J. Mol. Biol. , vol.310 , pp. 27-32
    • Gromiha, M.M.1    Selvaraj, S.2
  • 25
    • 67849124732 scopus 로고    scopus 로고
    • Protein Folding Rates and Stability: How Much Is There beyond Size
    • de Sancho, D.; Doshi, U.; Muñoz, V. Protein Folding Rates and Stability: How Much Is There Beyond Size J. Am. Chem. Soc. 2009, 131, 2074-2075
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 2074-2075
    • De Sancho, D.1    Doshi, U.2    Muñoz, V.3
  • 26
    • 0016696599 scopus 로고
    • Studies on Protein Folding, Unfolding and Fluctuations by Computer-Simulation 0.1. Effect of Specific Amino-Acid Sequence Represented by Specific Inter-Unit Interactions
    • Taketomi, H.; Ueda, Y.; Go, N. Studies on Protein Folding, Unfolding and Fluctuations by Computer-Simulation 0.1. Effect of Specific Amino-Acid Sequence Represented by Specific Inter-Unit Interactions Int. J. Pept. Protein Res. 1975, 7, 445-459
    • (1975) Int. J. Pept. Protein Res. , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 27
    • 0037166875 scopus 로고    scopus 로고
    • Exact Solution of the Muñoz-Eaton Model for Protein Folding
    • Bruscolini, P.; Pelizzola, A. Exact Solution of the Muñoz-Eaton Model for Protein Folding Phys. Rev. Lett. 2002, 88, 258101
    • (2002) Phys. Rev. Lett. , vol.88 , pp. 258101
    • Bruscolini, P.1    Pelizzola, A.2
  • 28
    • 0033554840 scopus 로고    scopus 로고
    • Engineering a Thermostable Protein Via Optimization of Charge-Charge Interactions on the Protein Surface
    • Loladze, V. V.; Ibarra-Molero, B.; Sanchez-Ruiz, J. M.; Makhatadze, G. I. Engineering a Thermostable Protein Via Optimization of Charge-Charge Interactions on the Protein Surface Biochemistry 1999, 38, 16419-16423
    • (1999) Biochemistry , vol.38 , pp. 16419-16423
    • Loladze, V.V.1    Ibarra-Molero, B.2    Sanchez-Ruiz, J.M.3    Makhatadze, G.I.4
  • 30
    • 77950388103 scopus 로고    scopus 로고
    • An Unlocking/Relocking Barrier in Conformational Fluctuations of Villin Headpiece Subdomain
    • Reiner, A.; Henklein, P.; Kiefhaber, T. An Unlocking/Relocking Barrier in Conformational Fluctuations of Villin Headpiece Subdomain Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 4955-4960
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 4955-4960
    • Reiner, A.1    Henklein, P.2    Kiefhaber, T.3
  • 31
    • 84865957909 scopus 로고    scopus 로고
    • Native State Conformational Heterogeneity of Hp35 Revealed by Time-Resolved Fret
    • Serrano, A. L.; Bilsel, O.; Gai, F. Native State Conformational Heterogeneity of Hp35 Revealed by Time-Resolved Fret J. Phys. Chem. B 2012, 116, 10631-10638
    • (2012) J. Phys. Chem. B , vol.116 , pp. 10631-10638
    • Serrano, A.L.1    Bilsel, O.2    Gai, F.3
  • 32
    • 34250802058 scopus 로고    scopus 로고
    • Rational Design, Structural and Thermodynamic Characterization of a Hyperstable Variant of the Villin Headpiece Helical Subdomain
    • Bi, Y.; Cho, J. H.; Kim, E. Y.; Shan, B.; Schindelin, H.; Raleigh, D. P. Rational Design, Structural and Thermodynamic Characterization of a Hyperstable Variant of the Villin Headpiece Helical Subdomain Biochemistry 2007, 46, 7497-7505
    • (2007) Biochemistry , vol.46 , pp. 7497-7505
    • Bi, Y.1    Cho, J.H.2    Kim, E.Y.3    Shan, B.4    Schindelin, H.5    Raleigh, D.P.6
  • 34
    • 15244350748 scopus 로고    scopus 로고
    • Stabilization of the Cold Shock Protein Cspb from Bacillus Subtilis by Evolutionary Optimization of Coulombic Interactions
    • Wunderlich, M.; Martin, A.; Schmid, F. X. Stabilization of the Cold Shock Protein Cspb from Bacillus Subtilis by Evolutionary Optimization of Coulombic Interactions J. Mol. Biol. 2005, 347, 1063-1076
    • (2005) J. Mol. Biol. , vol.347 , pp. 1063-1076
    • Wunderlich, M.1    Martin, A.2    Schmid, F.X.3
  • 36
    • 1942521649 scopus 로고    scopus 로고
    • Thermodynamics and Kinetics of Non-Native Interactions in Protein Folding: A Single Point Mutant Significantly Stabilizes the N-Terminal Domain of L9 by Modulating Non-Native Interactions in the Denatured State
    • Cho, J. H.; Sato, S.; Raleigh, D. P. Thermodynamics and Kinetics of Non-Native Interactions in Protein Folding: A Single Point Mutant Significantly Stabilizes the N-Terminal Domain of L9 by Modulating Non-Native Interactions in the Denatured State J. Mol. Biol. 2004, 338, 827-837
    • (2004) J. Mol. Biol. , vol.338 , pp. 827-837
    • Cho, J.H.1    Sato, S.2    Raleigh, D.P.3
  • 37
    • 25144470141 scopus 로고    scopus 로고
    • Mutational Analysis Demonstrates That Specific Electrostatic Interactions Can Play a Key Role in the Denatured State Ensemble of Proteins
    • Cho, J. H.; Raleigh, D. P. Mutational Analysis Demonstrates That Specific Electrostatic Interactions Can Play a Key Role in the Denatured State Ensemble of Proteins J. Mol. Biol. 2005, 353, 174-185
    • (2005) J. Mol. Biol. , vol.353 , pp. 174-185
    • Cho, J.H.1    Raleigh, D.P.2
  • 38
    • 70349422120 scopus 로고    scopus 로고
    • Nonnative Electrostatic Interactions Can Modulate Protein Folding: Molecular Dynamics with a Grain of Salt
    • Azia, A.; Levy, Y. Nonnative Electrostatic Interactions Can Modulate Protein Folding: Molecular Dynamics with a Grain of Salt J. Mol. Biol. 2009, 393, 527-542
    • (2009) J. Mol. Biol. , vol.393 , pp. 527-542
    • Azia, A.1    Levy, Y.2
  • 39
    • 0039116206 scopus 로고    scopus 로고
    • Structural Differences between Mesophilic, Moderately Thermophilic and Extremely Thermophilic Protein Subunits: Results of a Comprehensive Survey
    • Szilagyi, A.; Zavodszky, P. Structural Differences between Mesophilic, Moderately Thermophilic and Extremely Thermophilic Protein Subunits: Results of a Comprehensive Survey Structure 2000, 8, 493-504
    • (2000) Structure , vol.8 , pp. 493-504
    • Szilagyi, A.1    Zavodszky, P.2
  • 40
    • 0034017055 scopus 로고    scopus 로고
    • Factors Enhancing Protein Thermostability
    • Kumar, S.; Tsai, C. J.; Nussinov, R. Factors Enhancing Protein Thermostability Protein Eng. 2000, 13, 179-191
    • (2000) Protein Eng. , vol.13 , pp. 179-191
    • Kumar, S.1    Tsai, C.J.2    Nussinov, R.3
  • 41
    • 16244366490 scopus 로고    scopus 로고
    • Electrostatic Interactions Contribute to Reduced Heat Capacity Change of Unfolding in a Thermophilic Ribosomal Protein L30e
    • Lee, C. F.; Allen, M. D.; Bycroft, M.; Wong, K. B. Electrostatic Interactions Contribute to Reduced Heat Capacity Change of Unfolding in a Thermophilic Ribosomal Protein L30e J. Mol. Biol. 2005, 348, 419-431
    • (2005) J. Mol. Biol. , vol.348 , pp. 419-431
    • Lee, C.F.1    Allen, M.D.2    Bycroft, M.3    Wong, K.B.4
  • 42
    • 0035980242 scopus 로고    scopus 로고
    • Thermodynamic Basis for the Increased Thermodynamic Stability of Chey from the Hyperthermophile Thermotoga Maritima
    • Deutschman, W. A.; Dahlquist, F. W. Thermodynamic Basis for the Increased Thermodynamic Stability of Chey from the Hyperthermophile Thermotoga Maritima Biochemistry 2001, 40, 13107-13113
    • (2001) Biochemistry , vol.40 , pp. 13107-13113
    • Deutschman, W.A.1    Dahlquist, F.W.2
  • 44
    • 2442683149 scopus 로고    scopus 로고
    • The Folding Transition State of the Cold Shock Protein Is Strongly Polarized
    • Garcia-Mira, M. M.; Boehringer, D.; Schmid, F. X. The Folding Transition State of the Cold Shock Protein Is Strongly Polarized J. Mol. Biol. 2004, 339, 555-569
    • (2004) J. Mol. Biol. , vol.339 , pp. 555-569
    • Garcia-Mira, M.M.1    Boehringer, D.2    Schmid, F.X.3
  • 46
    • 0028947257 scopus 로고
    • Funnels, Pathways, and the Energy Landscape of Protein-Folding - A Synthesis
    • Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Funnels, Pathways, and the Energy Landscape of Protein-Folding-a Synthesis Proteins 1995, 21, 167-195
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 47
    • 37749052245 scopus 로고    scopus 로고
    • Prediction of Protein Stability Upon Point Mutations
    • Gromiha, M. M. Prediction of Protein Stability Upon Point Mutations Biochem. Soc. Trans. 2007, 35, 1569-1573
    • (2007) Biochem. Soc. Trans. , vol.35 , pp. 1569-1573
    • Gromiha, M.M.1
  • 48
    • 0036291145 scopus 로고    scopus 로고
    • Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations
    • Guerois, R.; Nielsen, J. E.; Serrano, L. Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations J. Mol. Biol. 2002, 320, 369-387
    • (2002) J. Mol. Biol. , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 49
    • 4544334447 scopus 로고    scopus 로고
    • Large-Scale Prediction of Protein Geometry and Stability Changes for Arbitrary Single Point Mutations
    • Bordner, A. J.; Abagyan, R. A. Large-Scale Prediction of Protein Geometry and Stability Changes for Arbitrary Single Point Mutations Proteins: Struct. Funct. Bioinf. 2004, 57, 400-413
    • (2004) Proteins: Struct. Funct. Bioinf. , vol.57 , pp. 400-413
    • Bordner, A.J.1    Abagyan, R.A.2
  • 50
    • 34249777526 scopus 로고    scopus 로고
    • Eris: An Automated Estimator of Protein Stability
    • Yin, S. Y.; Ding, F.; Dokholyan, N. V. Eris: An Automated Estimator of Protein Stability Nat. Methods 2007, 4, 466-467
    • (2007) Nat. Methods , vol.4 , pp. 466-467
    • Yin, S.Y.1    Ding, F.2    Dokholyan, N.V.3
  • 51
    • 79955866957 scopus 로고    scopus 로고
    • Popmusic 2.1: A Web Server for the Estimation of Protein Stability Changes Upon Mutation and Sequence Optimality
    • Dehouck, Y.; Kwasigroch, J. M.; Gilis, D.; Rooman, M. Popmusic 2.1: A Web Server for the Estimation of Protein Stability Changes Upon Mutation and Sequence Optimality. BMC Bioinf. 2011, 12.
    • (2011) BMC Bioinf. , vol.12
    • Dehouck, Y.1    Kwasigroch, J.M.2    Gilis, D.3    Rooman, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.