메뉴 건너뛰기




Volumn 59, Issue 23, 2016, Pages 10530-10548

Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands

Author keywords

[No Author keywords available]

Indexed keywords

CRYOPROTECTIVE AGENT; GLYCEROL; SURFACE WATER; THERMOLYSIN; LIGAND; PROTEIN; WATER;

EID: 85003422164     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/acs.jmedchem.6b00998     Document Type: Article
Times cited : (59)

References (81)
  • 1
    • 52049123291 scopus 로고    scopus 로고
    • Do Enthalpy and Entropy Distinguish First in Class from Best in Class?
    • Freire, E. Do Enthalpy and Entropy Distinguish First in Class from Best in Class? Drug Discovery Today 2008, 13, 869-874 10.1016/j.drudis.2008.07.005
    • (2008) Drug Discovery Today , vol.13 , pp. 869-874
    • Freire, E.1
  • 2
    • 77957229353 scopus 로고    scopus 로고
    • Thermodynamics Guided Lead Discovery and Optimization
    • Ferenczy, G. G.; Keseru, G. M. Thermodynamics Guided Lead Discovery and Optimization Drug Discovery Today 2010, 15, 919-932 10.1016/j.drudis.2010.08.013
    • (2010) Drug Discovery Today , vol.15 , pp. 919-932
    • Ferenczy, G.G.1    Keseru, G.M.2
  • 3
    • 74149083849 scopus 로고    scopus 로고
    • Adding Calorimetric Data to Decision Making in Lead Discovery: A Hot Tip
    • Ladbury, J. E.; Klebe, G.; Freire, E. Adding Calorimetric Data to Decision Making in Lead Discovery: A Hot Tip Nat. Rev. Drug Discovery 2010, 9, 23-27 10.1038/nrd3054
    • (2010) Nat. Rev. Drug Discovery , vol.9 , pp. 23-27
    • Ladbury, J.E.1    Klebe, G.2    Freire, E.3
  • 4
    • 78650750341 scopus 로고    scopus 로고
    • The Heat Is on: Thermodynamic Analysis in Fragment-Based Drug Discovery
    • Edink, E.; Jansen, C.; Leurs, R.; De Esch, I. J. P. The Heat Is on: Thermodynamic Analysis in Fragment-Based Drug Discovery Drug Discovery Today: Technol. 2010, 7, e189-e201 10.1016/j.ddtec.2010.12.001
    • (2010) Drug Discovery Today: Technol. , vol.7 , pp. e189-e201
    • Edink, E.1    Jansen, C.2    Leurs, R.3    De Esch, I.J.P.4
  • 5
    • 70349731747 scopus 로고    scopus 로고
    • A Thermodynamic Approach to the Affinity Optimization of Drug Candidates
    • Freire, E. A Thermodynamic Approach to the Affinity Optimization of Drug Candidates Chem. Biol. Drug Des. 2009, 74, 468-472 10.1111/j.1747-0285.2009.00880.x
    • (2009) Chem. Biol. Drug Des. , vol.74 , pp. 468-472
    • Freire, E.1
  • 6
    • 77955329488 scopus 로고    scopus 로고
    • Drug-Target Residence Time: Critical Information for Lead Optimization
    • Lu, H.; Tonge, P. J. Drug-Target Residence Time: Critical Information for Lead Optimization Curr. Opin. Chem. Biol. 2010, 14, 467-474 10.1016/j.cbpa.2010.06.176
    • (2010) Curr. Opin. Chem. Biol. , vol.14 , pp. 467-474
    • Lu, H.1    Tonge, P.J.2
  • 7
    • 84957845231 scopus 로고    scopus 로고
    • The Drug-Target Residence Time Model: A 10-Year Retrospective
    • Copeland, R. A. The Drug-Target Residence Time Model: A 10-Year Retrospective Nat. Rev. Drug Discovery 2016, 15, 87-95 10.1038/nrd.2015.18
    • (2016) Nat. Rev. Drug Discovery , vol.15 , pp. 87-95
    • Copeland, R.A.1
  • 8
    • 0024356301 scopus 로고
    • Rapid Measurement of Binding Constants and Heats of Binding Using a New Titration Calorimeter
    • Wiseman, T.; Williston, S.; Brandts, J. F.; Lin, L.-N. Rapid Measurement of Binding Constants and Heats of Binding Using a New Titration Calorimeter Anal. Biochem. 1989, 179, 131-137 10.1016/0003-2697(89)90213-3
    • (1989) Anal. Biochem. , vol.179 , pp. 131-137
    • Wiseman, T.1    Williston, S.2    Brandts, J.F.3    Lin, L.-N.4
  • 9
    • 0035442411 scopus 로고    scopus 로고
    • Direct Measurement of Protein Binding Energetics by Isothermal Titration Calorimetry
    • Leavitt, S.; Freire, E. Direct Measurement of Protein Binding Energetics by Isothermal Titration Calorimetry Curr. Opin. Struct. Biol. 2001, 11, 560-566 10.1016/S0959-440X(00)00248-7
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 560-566
    • Leavitt, S.1    Freire, E.2
  • 10
    • 27344436962 scopus 로고    scopus 로고
    • Measurements of Binding Thermodynamics in Drug Discovery
    • Holdgate, G. A.; Ward, W. H. J. Measurements of Binding Thermodynamics in Drug Discovery Drug Discovery Today 2005, 10, 1543-1550 10.1016/S1359-6446(05)03610-X
    • (2005) Drug Discovery Today , vol.10 , pp. 1543-1550
    • Holdgate, G.A.1    Ward, W.H.J.2
  • 11
    • 84926158682 scopus 로고    scopus 로고
    • Applying Thermodynamic Profiling in Lead Finding and Optimization
    • Klebe, G. Applying Thermodynamic Profiling in Lead Finding and Optimization Nat. Rev. Drug Discovery 2015, 14, 95-110 10.1038/nrd4486
    • (2015) Nat. Rev. Drug Discovery , vol.14 , pp. 95-110
    • Klebe, G.1
  • 12
    • 84940501243 scopus 로고    scopus 로고
    • Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?
    • Geschwindner, S.; Ulander, J.; Johansson, P. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip? J. Med. Chem. 2015, 58, 6321-6335 10.1021/jm501511f
    • (2015) J. Med. Chem. , vol.58 , pp. 6321-6335
    • Geschwindner, S.1    Ulander, J.2    Johansson, P.3
  • 13
    • 84878914295 scopus 로고    scopus 로고
    • Correlating Structure and Energetics in Protein-Ligand Interactions: Paradigms and Paradoxes
    • Martin, S. F.; Clements, J. H. Correlating Structure and Energetics in Protein-Ligand Interactions: Paradigms and Paradoxes Annu. Rev. Biochem. 2013, 82, 267-293 10.1146/annurev-biochem-060410-105819
    • (2013) Annu. Rev. Biochem. , vol.82 , pp. 267-293
    • Martin, S.F.1    Clements, J.H.2
  • 14
    • 84879925936 scopus 로고    scopus 로고
    • Molecular Determinants of Drug-Receptor Binding Kinetics
    • Pan, A. C.; Borhani, D. W.; Dror, R. O.; Shaw, D. E. Molecular Determinants of Drug-Receptor Binding Kinetics Drug Discovery Today 2013, 18, 667-673 10.1016/j.drudis.2013.02.007
    • (2013) Drug Discovery Today , vol.18 , pp. 667-673
    • Pan, A.C.1    Borhani, D.W.2    Dror, R.O.3    Shaw, D.E.4
  • 15
    • 48249102785 scopus 로고    scopus 로고
    • Calorimetry and Thermodynamics in Drug Design
    • Chaires, J. B. Calorimetry and Thermodynamics in Drug Design Annu. Rev. Biophys. 2008, 37, 135-151 10.1146/annurev.biophys.36.040306.132812
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 135-151
    • Chaires, J.B.1
  • 16
    • 33748563642 scopus 로고    scopus 로고
    • Designing Ligands to Bind Proteins
    • Whitesides, G. M.; Krishnamurthy, V. M. Designing Ligands to Bind Proteins Q. Rev. Biophys. 2005, 38, 385-395 10.1017/S0033583506004240
    • (2005) Q. Rev. Biophys. , vol.38 , pp. 385-395
    • Whitesides, G.M.1    Krishnamurthy, V.M.2
  • 17
    • 38849196324 scopus 로고    scopus 로고
    • Water as an Active Constituent in Cell Biology
    • Ball, P. Water as an Active Constituent in Cell Biology Chem. Rev. 2008, 108, 74-108 10.1021/cr068037a
    • (2008) Chem. Rev. , vol.108 , pp. 74-108
    • Ball, P.1
  • 18
    • 0030466444 scopus 로고    scopus 로고
    • Just Add Water! The Effect of Water on the Specificity of Protein-Ligand Binding Sites and Its Potential Application to Drug Design
    • Ladbury, J. E. Just Add Water! The Effect of Water on the Specificity of Protein-Ligand Binding Sites and Its Potential Application to Drug Design Chem. Biol. 1996, 3, 973-980 10.1016/S1074-5521(96)90164-7
    • (1996) Chem. Biol. , vol.3 , pp. 973-980
    • Ladbury, J.E.1
  • 19
    • 56549131177 scopus 로고    scopus 로고
    • The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design
    • Olsson, T. S. G.; Williams, M. A.; Pitt, W. R.; Ladbury, J. E. The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design J. Mol. Biol. 2008, 384, 1002-1017 10.1016/j.jmb.2008.09.073
    • (2008) J. Mol. Biol. , vol.384 , pp. 1002-1017
    • Olsson, T.S.G.1    Williams, M.A.2    Pitt, W.R.3    Ladbury, J.E.4
  • 20
    • 77953631827 scopus 로고    scopus 로고
    • A Medicinal Chemist’s Guide to Molecular Interactions
    • Bissantz, C.; Kuhn, B.; Stahl, M. A Medicinal Chemist’s Guide to Molecular Interactions J. Med. Chem. 2010, 53, 5061-5084 10.1021/jm100112j
    • (2010) J. Med. Chem. , vol.53 , pp. 5061-5084
    • Bissantz, C.1    Kuhn, B.2    Stahl, M.3
  • 22
    • 0032901515 scopus 로고    scopus 로고
    • Isothermal Titration Calorimetry and Differential Scanning Calorimetry as Complementary Tools to Invesitigate the Energetics of Biomolecular Recognition
    • Jelesarov, I.; Bosshard, H. R. Isothermal Titration Calorimetry and Differential Scanning Calorimetry as Complementary Tools to Invesitigate the Energetics of Biomolecular Recognition J. Mol. Recognit. 1999, 12, 3-18 10.1002/(SICI)1099-1352(199901/02)12:1<3::AID-JMR441>3.0.CO;2-6
    • (1999) J. Mol. Recognit. , vol.12 , pp. 3-18
    • Jelesarov, I.1    Bosshard, H.R.2
  • 23
    • 84863812540 scopus 로고    scopus 로고
    • Ligand Binding Stepwise Disrupts Water Network in Thrombin: Enthalpic and Entropic Changes Reveal Classical Hydrophobic Effect
    • Biela, A.; Sielaff, F.; Terwesten, F.; Heine, A.; Steinmetzer, T.; Klebe, G. Ligand Binding Stepwise Disrupts Water Network in Thrombin: Enthalpic and Entropic Changes Reveal Classical Hydrophobic Effect J. Med. Chem. 2012, 55, 6094-6110 10.1021/jm300337q
    • (2012) J. Med. Chem. , vol.55 , pp. 6094-6110
    • Biela, A.1    Sielaff, F.2    Terwesten, F.3    Heine, A.4    Steinmetzer, T.5    Klebe, G.6
  • 24
    • 34447108978 scopus 로고    scopus 로고
    • Water, Water Everywhere - except Where It Matters?
    • Homans, S. W. Water, Water Everywhere-except Where It Matters? Drug Discovery Today 2007, 12, 534-539 10.1016/j.drudis.2007.05.004
    • (2007) Drug Discovery Today , vol.12 , pp. 534-539
    • Homans, S.W.1
  • 25
    • 77956583186 scopus 로고    scopus 로고
    • How Can Hydrophobic Association Be Enthalpy-Driven?
    • Setny, P.; Baron, R.; McCammon, J. A. How Can Hydrophobic Association Be Enthalpy-Driven? J. Chem. Theory Comput. 2010, 6, 2866-2871 10.1021/ct1003077
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 2866-2871
    • Setny, P.1    Baron, R.2    McCammon, J.A.3
  • 26
    • 78049348054 scopus 로고    scopus 로고
    • Molecular Binding: Under Water’s Influence
    • Hummer, G. Molecular Binding: Under Water’s Influence Nat. Chem. 2010, 2, 906-907 10.1038/nchem.885
    • (2010) Nat. Chem. , vol.2 , pp. 906-907
    • Hummer, G.1
  • 27
    • 84900498772 scopus 로고    scopus 로고
    • Is It the Shape of the Cavity, or the Shape of the Water in the Cavity?
    • Snyder, P. W.; Lockett, M. R.; Moustakas, D. T.; Whitesides, G. M. Is It the Shape of the Cavity, or the Shape of the Water in the Cavity? Eur. Phys. J.: Spec. Top. 2014, 223, 853-891 10.1140/epjst/e2013-01818-y
    • (2014) Eur. Phys. J.: Spec. Top. , vol.223 , pp. 853-891
    • Snyder, P.W.1    Lockett, M.R.2    Moustakas, D.T.3    Whitesides, G.M.4
  • 29
    • 84864400966 scopus 로고    scopus 로고
    • Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-Additivity of Functional Group Contributions in Protein-Ligand Binding
    • Biela, A.; Betz, M.; Heine, A.; Klebe, G. Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-Additivity of Functional Group Contributions in Protein-Ligand Binding ChemMedChem 2012, 7, 1423-1434 10.1002/cmdc.201200206
    • (2012) ChemMedChem , vol.7 , pp. 1423-1434
    • Biela, A.1    Betz, M.2    Heine, A.3    Klebe, G.4
  • 30
    • 84873351927 scopus 로고    scopus 로고
    • Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin
    • Biela, A.; Nasief, N. N.; Betz, M.; Heine, A.; Hangauer, D.; Klebe, G. Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin Angew. Chem., Int. Ed. 2013, 52, 1822-1828 10.1002/anie.201208561
    • (2013) Angew. Chem., Int. Ed. , vol.52 , pp. 1822-1828
    • Biela, A.1    Nasief, N.N.2    Betz, M.3    Heine, A.4    Hangauer, D.5    Klebe, G.6
  • 32
    • 84898006931 scopus 로고    scopus 로고
    • Methyl, Ethyl, Propyl, Butyl: Futile but Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors
    • Krimmer, S. G.; Betz, M.; Heine, A.; Klebe, G. Methyl, Ethyl, Propyl, Butyl: Futile but Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors ChemMedChem 2014, 9, 833-846 10.1002/cmdc.201400013
    • (2014) ChemMedChem , vol.9 , pp. 833-846
    • Krimmer, S.G.1    Betz, M.2    Heine, A.3    Klebe, G.4
  • 34
    • 58149103584 scopus 로고    scopus 로고
    • The Thermolysin Family (M4) of Enzymes: Therapeutic and Biotechnological Potential
    • Adekoya, O. A.; Sylte, I. The Thermolysin Family (M4) of Enzymes: Therapeutic and Biotechnological Potential Chem. Biol. Drug Des. 2009, 73, 7-16 10.1111/j.1747-0285.2008.00757.x
    • (2009) Chem. Biol. Drug Des. , vol.73 , pp. 7-16
    • Adekoya, O.A.1    Sylte, I.2
  • 35
    • 79960670878 scopus 로고    scopus 로고
    • The Role of Calcium Ions in the Stability and Instability of a Thermolysin-like Protease
    • Eijsink, V. G. H.; Matthews, B. W.; Vriend, G. The Role of Calcium Ions in the Stability and Instability of a Thermolysin-like Protease Protein Sci. 2011, 20, 1346-1355 10.1002/pro.670
    • (2011) Protein Sci. , vol.20 , pp. 1346-1355
    • Eijsink, V.G.H.1    Matthews, B.W.2    Vriend, G.3
  • 36
    • 0020321280 scopus 로고
    • Angiotensin-Converting Enzyme Inhibitors: Medicinal Chemistry and Biological Actions
    • Petrillo, E. W. J.; Ondetti, M. A. Angiotensin-Converting Enzyme Inhibitors: Medicinal Chemistry and Biological Actions Med. Res. Rev. 1982, 2, 1-41 10.1002/med.2610020103
    • (1982) Med. Res. Rev. , vol.2 , pp. 1-41
    • Petrillo, E.W.J.1    Ondetti, M.A.2
  • 37
    • 0028158656 scopus 로고
    • Inhibition of Thermolysin and Neutral Endopeptidase 24.11 by a Novel Glutaramide Derivative: X-Ray Structure Determination of the Thermolysin-Inhibitor Complex
    • Holland, D. R.; Barclay, P. L.; Danilewicz, J. C.; Matthews, B. W.; James, K. Inhibition of Thermolysin and Neutral Endopeptidase 24.11 by a Novel Glutaramide Derivative: X-Ray Structure Determination of the Thermolysin-Inhibitor Complex Biochemistry 1994, 33, 51-56 10.1021/bi00167a007
    • (1994) Biochemistry , vol.33 , pp. 51-56
    • Holland, D.R.1    Barclay, P.L.2    Danilewicz, J.C.3    Matthews, B.W.4    James, K.5
  • 38
    • 0001594721 scopus 로고    scopus 로고
    • Entropy-Enthalpy Compensation in Solvation and Ligand Binding Revisited
    • Gallicchio, E.; Kubo, M. M.; Levy, R. M. Entropy-Enthalpy Compensation in Solvation and Ligand Binding Revisited J. Am. Chem. Soc. 1998, 120, 4526-4527 10.1021/ja974061h
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 4526-4527
    • Gallicchio, E.1    Kubo, M.M.2    Levy, R.M.3
  • 39
    • 84860390480 scopus 로고    scopus 로고
    • Extent of Enthalpy-Entropy Compensation in Protein-Ligand Interactions
    • Olsson, T. S. G.; Ladbury, J. E.; Pitt, W. R.; Williams, M. A. Extent of Enthalpy-Entropy Compensation in Protein-Ligand Interactions Protein Sci. 2011, 20, 1607-1618 10.1002/pro.692
    • (2011) Protein Sci. , vol.20 , pp. 1607-1618
    • Olsson, T.S.G.1    Ladbury, J.E.2    Pitt, W.R.3    Williams, M.A.4
  • 40
    • 84877768087 scopus 로고    scopus 로고
    • Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
    • Chodera, J. D.; Mobley, D. L. Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design Annu. Rev. Biophys. 2013, 42, 121-142 10.1146/annurev-biophys-083012-130318
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 121-142
    • Chodera, J.D.1    Mobley, D.L.2
  • 41
    • 84955472225 scopus 로고    scopus 로고
    • Impact of Surface Water Layers on Protein-Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case
    • Betz, M.; Wulsdorf, T.; Krimmer, S. G.; Klebe, G. Impact of Surface Water Layers on Protein-Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case J. Chem. Inf. Model. 2016, 56, 223-233 10.1021/acs.jcim.5b00621
    • (2016) J. Chem. Inf. Model. , vol.56 , pp. 223-233
    • Betz, M.1    Wulsdorf, T.2    Krimmer, S.G.3    Klebe, G.4
  • 42
    • 0028011543 scopus 로고
    • Kinetic and Mechanistic Characterization of an Efficient Hydrolytic Antibody: Evidence for the Formation of an Acyl Intermediate
    • Guo, J.; Huang, W.; Scanlan, T. S. Kinetic and Mechanistic Characterization of an Efficient Hydrolytic Antibody: Evidence for the Formation of an Acyl Intermediate J. Am. Chem. Soc. 1994, 116, 6062-6069 10.1021/ja00093a002
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 6062-6069
    • Guo, J.1    Huang, W.2    Scanlan, T.S.3
  • 43
    • 0023667724 scopus 로고
    • Slow- and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding: Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues
    • Holden, H. M.; Tronrud, D. E.; Monzingo, A. F.; Weaver, L. H.; Matthews, B. W. Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding: Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues Biochemistry 1987, 26, 8542-8553 10.1021/bi00400a008
    • (1987) Biochemistry , vol.26 , pp. 8542-8553
    • Holden, H.M.1    Tronrud, D.E.2    Monzingo, A.F.3    Weaver, L.H.4    Matthews, B.W.5
  • 44
    • 77956268336 scopus 로고    scopus 로고
    • Displacement of Disordered Water Molecules from Hydrophobic Pocket Creates Enthalpic Signature: Binding of Phosphonamidate to the S1′-pocket of Thermolysin
    • Englert, L.; Biela, A.; Zayed, M.; Heine, A.; Hangauer, D.; Klebe, G. Displacement of Disordered Water Molecules from Hydrophobic Pocket Creates Enthalpic Signature: Binding of Phosphonamidate to the S1′-pocket of Thermolysin Biochim. Biophys. Acta, Gen. Subj. 2010, 1800, 1192-1202 10.1016/j.bbagen.2010.06.009
    • (2010) Biochim. Biophys. Acta, Gen. Subj. , vol.1800 , pp. 1192-1202
    • Englert, L.1    Biela, A.2    Zayed, M.3    Heine, A.4    Hangauer, D.5    Klebe, G.6
  • 45
    • 84944352692 scopus 로고    scopus 로고
    • Thermodynamics of Protein-Ligand Interactions as a Reference for Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data
    • Krimmer, S. G.; Klebe, G. Thermodynamics of Protein-Ligand Interactions as a Reference for Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data J. Comput.-Aided Mol. Des. 2015, 29, 867-883 10.1007/s10822-015-9867-y
    • (2015) J. Comput.-Aided Mol. Des. , vol.29 , pp. 867-883
    • Krimmer, S.G.1    Klebe, G.2
  • 46
    • 0033460194 scopus 로고    scopus 로고
    • Correlation between Occupancy and B Factor of Water Molecules in Protein Crystal Structures
    • Carugo, O. Correlation between Occupancy and B Factor of Water Molecules in Protein Crystal Structures Protein Eng., Des. Sel. 1999, 12, 1021-1024 10.1093/protein/12.12.1021
    • (1999) Protein Eng., Des. Sel. , vol.12 , pp. 1021-1024
    • Carugo, O.1
  • 49
    • 0030598828 scopus 로고    scopus 로고
    • Global Analysis of a Macromolecular Interaction Measured on BIAcore
    • Roden, L. D.; Myszka, D. G. Global Analysis of a Macromolecular Interaction Measured on BIAcore Biochem. Biophys. Res. Commun. 1996, 225, 1073-1077 10.1006/bbrc.1996.1297
    • (1996) Biochem. Biophys. Res. Commun. , vol.225 , pp. 1073-1077
    • Roden, L.D.1    Myszka, D.G.2
  • 50
    • 0342813129 scopus 로고    scopus 로고
    • Experimental Design for Kinetic Analysis of Protein-Protein Interactions with Surface Plasmon Resonance Biosensors
    • Karlsson, R.; Fält, A. Experimental Design for Kinetic Analysis of Protein-Protein Interactions with Surface Plasmon Resonance Biosensors J. Immunol. Methods 1997, 200, 121-133 10.1016/S0022-1759(96)00195-0
    • (1997) J. Immunol. Methods , vol.200 , pp. 121-133
    • Karlsson, R.1    Fält, A.2
  • 51
    • 0033081137 scopus 로고    scopus 로고
    • How Many Water Molecules Can Be Detected by Protein Crystallography?
    • Carugo, O.; Bordo, D. How Many Water Molecules Can Be Detected by Protein Crystallography? Acta Crystallogr., Sect. D: Biol. Crystallogr. 1999, 55, 479-483 10.1107/S0907444998012086
    • (1999) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.55 , pp. 479-483
    • Carugo, O.1    Bordo, D.2
  • 52
    • 84870579518 scopus 로고    scopus 로고
    • Entropy-Enthalpy Transduction Caused by Conformational Shifts Can Obscure the Forces Driving Protein-Ligand Binding
    • Fenley, A. T.; Muddana, H. S.; Gilson, M. K. Entropy-Enthalpy Transduction Caused by Conformational Shifts Can Obscure the Forces Driving Protein-Ligand Binding Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 20006-200011 10.1073/pnas.1213180109
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 20006-200011
    • Fenley, A.T.1    Muddana, H.S.2    Gilson, M.K.3
  • 54
    • 67650082452 scopus 로고    scopus 로고
    • Water Polygons in High-Resolution Protein Crystal Structures
    • Lee, J.; Kim, S. H. Water Polygons in High-Resolution Protein Crystal Structures Protein Sci. 2009, 18, 1370-1376 10.1002/pro.162
    • (2009) Protein Sci. , vol.18 , pp. 1370-1376
    • Lee, J.1    Kim, S.H.2
  • 55
    • 84873876347 scopus 로고    scopus 로고
    • Identification of Structural-Kinetic and Structural-Thermodynamic Relationships for Thrombin Inhibitors
    • Winquist, J.; Geschwindner, S.; Xue, Y.; Gustavsson, L.; Musil, D.; Deinum, J.; Danielson, U. H. Identification of Structural-Kinetic and Structural-Thermodynamic Relationships for Thrombin Inhibitors Biochemistry 2013, 52, 613-626 10.1021/bi301333z
    • (2013) Biochemistry , vol.52 , pp. 613-626
    • Winquist, J.1    Geschwindner, S.2    Xue, Y.3    Gustavsson, L.4    Musil, D.5    Deinum, J.6    Danielson, U.H.7
  • 56
    • 84966606067 scopus 로고    scopus 로고
    • Chemical Computing Group Inc. Montreal, QC (Canada)
    • Molecular Operating Environment (MOE); Chemical Computing Group Inc.: Montreal, QC (Canada), 2014.
    • (2014) Molecular Operating Environment (MOE)
  • 57
    • 3042524904 scopus 로고
    • A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model
    • Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model J. Phys. Chem. 1993, 97, 10269-10280 10.1021/j100142a004
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 60
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual Molecular Dynamics
    • Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38 10.1016/0263-7855(96)00018-5
    • (1996) J. Mol. Graphics , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 61
    • 0020462668 scopus 로고
    • Structure of Thermolysin Refined at 1.6 Å Resolution
    • Holmes, M. A.; Matthews, B. W. Structure of Thermolysin Refined at 1.6 Å Resolution J. Mol. Biol. 1982, 160, 623-639 10.1016/0022-2836(82)90319-9
    • (1982) J. Mol. Biol. , vol.160 , pp. 623-639
    • Holmes, M.A.1    Matthews, B.W.2
  • 66
    • 0026489329 scopus 로고
    • Structural Comparison Suggests That Thermolysin and Related Neutral Proteases Undergo Hinge-Bending Motion during Catalysis
    • Holland, D. R.; Tronrud, D. E.; Pley, H. W.; Flaherty, K. M.; Stark, W.; Jansonius, J. N.; McKay, D. B.; Matthews, B. W. Structural Comparison Suggests That Thermolysin and Related Neutral Proteases Undergo Hinge-Bending Motion during Catalysis Biochemistry 1992, 31, 11310-11316 10.1021/bi00161a008
    • (1992) Biochemistry , vol.31 , pp. 11310-11316
    • Holland, D.R.1    Tronrud, D.E.2    Pley, H.W.3    Flaherty, K.M.4    Stark, W.5    Jansonius, J.N.6    McKay, D.B.7    Matthews, B.W.8
  • 69
    • 70349597601 scopus 로고    scopus 로고
    • Electronic Ligand Builder and Optimization Workbench (eLBOW): A Tool for Ligand Coordinate and Restraint Generation
    • Moriarty, N. W.; Grosse-Kunstleve, R. W.; Adams, P. D. Electronic Ligand Builder and Optimization Workbench (eLBOW): A Tool for Ligand Coordinate and Restraint Generation Acta Crystallogr., Sect. D: Biol. Crystallogr. 2009, 65, 1074-1080 10.1107/S0907444909029436
    • (2009) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.65 , pp. 1074-1080
    • Moriarty, N.W.1    Grosse-Kunstleve, R.W.2    Adams, P.D.3
  • 71
    • 84859573207 scopus 로고    scopus 로고
    • Designing Isothermal Titration Calorimetry Experiments for the Study of 1:1 Binding: Problems with The “standard Protocol.
    • Tellinghuisen, J. Designing Isothermal Titration Calorimetry Experiments for the Study of 1:1 Binding: Problems with The “standard Protocol. Anal. Biochem. 2012, 424, 211-220 10.1016/j.ab.2011.12.035
    • (2012) Anal. Biochem. , vol.424 , pp. 211-220
    • Tellinghuisen, J.1
  • 72
    • 0842303040 scopus 로고    scopus 로고
    • The Role of Backlash in The “first Injection Anomaly” in Isothermal Titration Calorimetry
    • Mizoue, L. S.; Tellinghuisen, J. The Role of Backlash in The “first Injection Anomaly” in Isothermal Titration Calorimetry Anal. Biochem. 2004, 326, 125-127 10.1016/j.ab.2003.10.048
    • (2004) Anal. Biochem. , vol.326 , pp. 125-127
    • Mizoue, L.S.1    Tellinghuisen, J.2
  • 73
    • 84861840835 scopus 로고    scopus 로고
    • High-Precision Isothermal Titration Calorimetry with Automated Peak Shape Analysis
    • Keller, S.; Vargas, C.; Zhao, H.; Piszczek, G.; Brautigam, C. A.; Schuck, P. High-Precision Isothermal Titration Calorimetry with Automated Peak Shape Analysis Anal. Chem. 2012, 84, 5066-5073 10.1021/ac3007522
    • (2012) Anal. Chem. , vol.84 , pp. 5066-5073
    • Keller, S.1    Vargas, C.2    Zhao, H.3    Piszczek, G.4    Brautigam, C.A.5    Schuck, P.6
  • 74
    • 33845937672 scopus 로고    scopus 로고
    • Studying Multisite Binary and Ternary Protein Interactions by Global Analysis of Isothermal Titration Calorimetry Data in SEDPHAT: Application to Adaptor Protein Complexes in Cell Signaling
    • Houtman, J. C. D.; Brown, P. H.; Bowden, B.; Yamaguchi, H.; Appella, E.; Samelson, L. E.; Schuck, P. Studying Multisite Binary and Ternary Protein Interactions by Global Analysis of Isothermal Titration Calorimetry Data in SEDPHAT: Application to Adaptor Protein Complexes in Cell Signaling Protein Sci. 2007, 16, 30-42 10.1110/ps.062558507
    • (2007) Protein Sci. , vol.16 , pp. 30-42
    • Houtman, J.C.D.1    Brown, P.H.2    Bowden, B.3    Yamaguchi, H.4    Appella, E.5    Samelson, L.E.6    Schuck, P.7
  • 75
    • 84948575628 scopus 로고    scopus 로고
    • Calculations and Publication-Quality Illustrations for Analytical Ultracentrifugation Data
    • Brautigam, C. A. Calculations and Publication-Quality Illustrations for Analytical Ultracentrifugation Data Methods Enzymol. 2015, 562, 109-133 10.1016/bs.mie.2015.05.001
    • (2015) Methods Enzymol. , vol.562 , pp. 109-133
    • Brautigam, C.A.1
  • 76
    • 34548232365 scopus 로고    scopus 로고
    • Inference of Macromolecular Assemblies from Crystalline State
    • Krissinel, E.; Henrick, K. Inference of Macromolecular Assemblies from Crystalline State J. Mol. Biol. 2007, 372, 774-797 10.1016/j.jmb.2007.05.022
    • (2007) J. Mol. Biol. , vol.372 , pp. 774-797
    • Krissinel, E.1    Henrick, K.2
  • 78
    • 79953314466 scopus 로고    scopus 로고
    • Fconv: Format Conversion, Manipulation and Feature Computation of Molecular Data
    • Neudert, G.; Klebe, G. Fconv: Format Conversion, Manipulation and Feature Computation of Molecular Data Bioinformatics 2011, 27, 1021-1022 10.1093/bioinformatics/btr055
    • (2011) Bioinformatics , vol.27 , pp. 1021-1022
    • Neudert, G.1    Klebe, G.2
  • 79
    • 0000243829 scopus 로고
    • PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures
    • Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures J. Appl. Crystallogr. 1993, 26, 283-291 10.1107/S0021889892009944
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 80
    • 0000252066 scopus 로고
    • The γ Turn. Evidence for a New Folded Conformation in Proteins
    • Matthews, B. W. The γ Turn. Evidence for a New Folded Conformation in Proteins Macromolecules 1972, 5, 818-819 10.1021/ma60030a031
    • (1972) Macromolecules , vol.5 , pp. 818-819
    • Matthews, B.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.