Limiting assumptions in structure-based design: Binding entropy

Journal of Computer-Aided Molecular Design

Volumn 26, Issue 1, 2012, Pages 3-8

  Marshall, Garland R ^a,b  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGANDS;

ATOMIC LEVELS; HIV-1 PROTEASE; LIGAND BINDING; STRUCTURE-BASED DESIGNS;

ENTROPY;

HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE;

ANALYTIC METHOD; BINDING AFFINITY; BINDING KINETICS; DOUBLE ELECTRON ELECTRON RESONANCE; ENTROPY; ENZYME ACTIVITY; ENZYME BINDING; ENZYME LOCALIZATION; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SYNTHESIS; INTERMETHOD COMPARISON; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN INTERACTION; RECEPTOR BINDING; REVIEW;

EID: 84857456082     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9494-1     Document Type: Review

References (27)

1. JA Feng GR Marshall 2010 SKATE: a docking program that decouples systematic sampling from scoring J Comput Chem 31 2540 2554 10.1002/jcc.21545 1:CAS:528:DC%2BC3cXhtVyitbbI
2. JL Kear ME Blackburn AM Veloro BM Dunn GE Fanucci 2009 Subtype polymorphisms among HIV-1 protease variants confer altered flap conformations and flexibility J Am Chem Soc 131 14650 14651 10.1021/ja907088a 1:CAS:528:DC%2BD1MXhtF2lurrP
3. ME Blackburn AM Veloro GE Fanucci 2009 Monitoring inhibitor-induced conformational population shifts in HIV-1 protease by pulsed EPR spectroscopy Biochemistry 48 8765 8767 10.1021/bi901201q 1:CAS:528:DC%2BD1MXhtVartbvJ
4. L Galiano F Ding AM Veloro ME Blackburn C Simmerling GE Fanucci 2009 Drug pressure selected mutations in HIV-1 protease alter flap conformations J Am Chem Soc 131 430 431 10.1021/ja807531v 1:CAS:528:DC%2BD1cXhsFantbrE
5. VY Torbeev H Raghuraman K Mandal S Senapati E Perozo SB Kent 2009 Dynamics of "flap" structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy J Am Chem Soc 131 884 885 10.1021/ja806526z 1:CAS:528:DC%2BD1MXnt1Wj
6. JE Banham CM Baker S Ceola IJ Day GH Grant EJ Groenen CT Rodgers G Jeschke CR Timmel 2008 Distance measurements in the borderline region of applicability of CW EPR and DEER: a model study on a homologous series of spin-labelled peptides J Magn Reson 191 202 218 10.1016/j.jmr.2007.11.023 1:CAS:528:DC%2BD1cXktVSit7k%3D
7. G Jeschke A Koch U Jonas A Godt 2002 Direct conversion of EPR dipolar time evolution data to distance distributions J Magn Reson 155 72 82 10.1006/jmre.2001.2498 1:CAS:528:DC%2BD38Xis1yhtb8%3D
8. CJ Lopez MR Fleissner Z Guo AK Kusnetzow WL Hubbell 2009 Osmolyte perturbation reveals conformational equilibria in spin-labeled proteins Protein Sci 18 1637 1652 10.1002/pro.180 1:CAS:528:DC%2BD1MXpt1Cmu7k%3D
9. JE Lovett AM Bowen CR Timmel MW Jones JR Dilworth D Caprotti SG Bell LL Wong J Harmer 2009 Structural information from orientationally selective DEER spectroscopy Phys Chem Chem Phys 11 6840 6848 10.1039/b907010a 1:CAS:528:DC%2BD1MXptF2rsLY%3D
10. YW Chiang PP Borbat JH Freed 2005 The determination of pair distance distributions by pulsed ESR using Tikhonov regularization J Magn Reson 172 279 295 10.1016/j.jmr.2004.10.012 1:CAS:528:DC%2BD2MXksVCltQ%3D%3D (Pubitemid 40072533)
11. R Ward A Bowman H El-Mkami T Owen-Hughes DG Norman 2009 Long distance PELDOR measurements on the histone core particle J Am Chem Soc 131 1348 1349 10.1021/ja807918f 1:CAS:528:DC%2BD1MXkt1yjsw%3D%3D
12. F Ding M Layten C Simmerling 2008 Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments J Am Chem Soc 130 7184 7185 10.1021/ja800893d 1:CAS:528: DC%2BD1cXmtVGhtLg%3D (Pubitemid 351813185)
13. JE Lovett M Hoffmann A Cnossen AT Shutter HJ Hogben JE Warren SI Pascu CW Kay CR Timmel HL Anderson 2009 Probing flexibility in porphyrin-based molecular wires using double electron electron resonance J Am Chem Soc 131 13852 13859 10.1021/ja905796z 1:CAS:528:DC%2BD1MXhtV2murzI
14. L Galiano M Bonora GE Fanucci 2007 Interflap distances in HIV-1 protease determined by pulsed EPR measurements J Am Chem Soc 129 11004 11005 10.1021/ja073684k 1:CAS:528:DC%2BD2sXptFSmsL4%3D (Pubitemid 47435689)
15. 10-helical conformation of alanine-based peptides in aqueous solution: an electron spin resonance investigation J Am Chem Soc 117 10555 10562 10.1021/ja00147a018 1:CAS:528:DyaK2MXosVKqtbo%3D
16. L Galiano M Bonora GE Fanucci 2007 Interflap distances in HIV-1 protease determined by pulsed EPR measurements J Am Chem Soc 129 11004 11005 10.1021/ja073684k 1:CAS:528:DC%2BD2sXptFSmsL4%3D (Pubitemid 47435689)
17. YT Tang GR Marshall 2011 PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements J Chem Inf Model 51 214 228 10.1021/ci100257s 1:CAS:528: DC%2BC3MXivFeiug%3D%3D
18. SF Martin 2007 Preorganization in biological systems: are conformational constraints worth the energy? Pure Appl Chem 79 193 200 10.1351/pac200779020193 1:CAS:528:DC%2BD2sXhvVKqtrg%3D
19. AP Benfield MG Teresk HR Plake JE DeLorbe LE Millspaugh SF Martin 2006 Ligand preorganization may be accompanied by entropic penalties in protein-ligand interactions Angew Chem Int Ed Engl 45 6830 6835 10.1002/anie.200600844 1:CAS:528:DC%2BD28XhtFOqsLbO (Pubitemid 44654469)
20. AP Benfield BB Whiddon JH Clements SF Martin 2007 Structural and energetic aspects of Grb2-SH2 domain-swapping Arch Biochem Biophys 462 47 53 10.1016/j.abb.2007.03.010 1:CAS:528:DC%2BD2sXlsF2msbg%3D (Pubitemid 46755137)
21. JH Clements JE DeLorbe AP Benfield SF Martin 2010 Binding of flexible and constrained ligands to the Grb2 SH2 domain: structural effects of ligand preorganization Acta Crystallogr D Biol Crystallogr 66 1101 1115 10.1107/S0907444910035584
22. JE DeLorbe JH Clements MG Teresk AP Benfield HR Plake LE Millspaugh SF Martin 2009 Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization J Am Chem Soc 131 16758 16770 10.1021/ja904698q 1:CAS:528:DC%2BD1MXhtlGjsbnF
23. JE Delorbe JH Clements BB Whiddon SF Martin 2010 Thermodynamic and structural effects of macrocyclization as a constraining method in protein-ligand interactions ACS Med Chem Lett 1 448 452 10.1021/ml100142y 1:CAS:528:DC%2BC3cXhtVamtrfF
24. JM Ward NM Gorenstein J Tian SF Martin CB Post 2010 Constraining binding hot spots: NMR and molecular dynamics simulations provide a structural explanation for enthalpy-entropy compensation in SH2-ligand binding J Am Chem Soc 132 11058 11070 10.1021/ja910535j 1:CAS:528:DC%2BC3cXpsVWlsbk%3D
25. CR Kissinger AK Dunker E Shakhnovich 1999 Disorder in protein structure and function Pac Symp Biocomput 4 517 519
26. VN Uversky CJ Oldfield AK Dunker 2008 Intrinsically disordered proteins in human diseases: introducing the D2 concept Annu Rev Biophys 37 215 246 10.1146/annurev.biophys.37.032807.125924 1:CAS:528:DC%2BD1cXnsVGltbc%3D
27. G Jeschke 2002 Distance measurements in the nanometer range by pulse EPR Chemphyschem 3 927 932 10.1002/1439-7641(20021115)3:11<927::AID-CPHC927>3. 0.CO;2-Q 1:CAS:528:DC%2BD38Xptlaks74%3D