50. Li Z, Lazaridis T (2005) The effect of water displacement on binding thermodynamics:
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51. Young T, Abel R, Kim B et al (2007) Motifs for molecular recognition exploiting
hydrophobic enclosure in protein–ligand binding. Proc Natl Acad Sci 104:808–813. https://
doi.org/10.1073/pnas.0610202104
52. Snyder PW, Mecinovic J, Moustakas DT et al (2011) Mechanism of the hydrophobic effect
in the biomolecular recognition of arylsulfonamides by carbonic anhydrase. Proc Natl Acad
Sci 108:17889–17894. https://doi.org/10.1073/pnas.1114107108
53. Sánchez R, Sali A (1997) Advances in comparative protein-structure modelling. Curr Opin
Struct Biol 7:206–214
54. Eswar N, John B, Mirkovic N et al (2003) Tools for comparative protein structure modeling
and analysis. Nucl Acids Res 31:3375–3380
55. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to
check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291.
https://doi.org/10.1107/s0021889892009944
56. Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol
Graph 8:52–6, 29
57. McKinney JD, Zu Bentrup K Höner, Muñoz-Elias EJ et al (2000) Persistence of
Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt
enzyme isocitrate lyase. Nature 406:735–738. https://doi.org/10.1038/35021074
58. Tanjore Soundarajan Balganesh; Santanu Datta; Indira Ghosh (2004) WO2004087943A1
59. Nelson K, Wang FS, Boyd EF, Selander RK (1997) Size and sequence polymorphism in the
isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella
enterica and Escherichia coli. Genetics 147:1509–1520
60. Garnak M, Reeves H (1979) Phosphorylation of isocitrate dehydrogenase of Escherichia
coli. Science 203(80):1111–1112. https://doi.org/10.1126/science.34215
61. Vinekar R, Verma C, Ghosh I (2012) Functional relevance of dynamic properties of dimeric
NADP-dependent isocitrate dehydrogenases. BMC Bioinform 13:S2. https://doi.org/10.
1186/1471-2105-13-s17-s2
62. Vinekar R, Ghosh I (2009) Determination of phosphorylation sites for NADP-specific
isocitrate dehydrogenase from Mycobacterium tuberculosis. J Biomol Struct Dyn 26:741–
754. https://doi.org/10.1080/07391102.2009.10507286
63. Av-Gay Y, Everett M (2000) The eukaryotic-like Ser/Thr protein kinases of Mycobacterium
tuberculosis. Trends Microbiol 8:238–244
64. Hurley JH, Thorsness PE, Ramalingam V et al (1989) Structure of a bacterial enzyme
regulated by phosphorylation, isocitrate dehydrogenase. Proc Natl Acad Sci U S A 86:8635–
8639. https://doi.org/10.1073/pnas.86.22.8635
65. Ceccarelli C, Grodsky NB, Ariyaratne N et al (2002) Crystal structure of porcine
mitochondrial NADP
+ -dependent isocitrate dehydrogenase complexed with Mn
2+ and
isocitrate: Insights into the enzyme mechanism. J Biol Chem 277:43454–43462. https://doi.
org/10.1074/jbc.m207306200
66. Quartararo CE, Hazra S, Hadi T, Blanchard JS (2013) Structural, kinetic and chemical
mechanism of isocitrate dehydrogenase-1 from Mycobacterium tuberculosis. Biochemistry
52:1765–1775. https://doi.org/10.1021/bi400037w
67. Hardin C, Pogorelov TV, Luthey-Schulten Z (2002) Ab initio protein structure prediction.
Curr Opin Struct Biol 12:176–181
68. Bonneau R, Baker D (2001) Ab initio protein structure prediction. Annu Rev Biophys
Biomol Struct 30:173–189
69. Moult J, Fidelis K, Kryshtafovych A et al (2017) Critical assessment of methods of protein
structure prediction (CASP)—round XII. Proteins Struct Funct Bioinform 82:1–6
70. Singh A, Kaushik R, Mishra A et al (2016) ProTSAV: a protein tertiary structure analysis
and validation server. Biochim Biophys Acta Proteins Proteomics 1864:11–19. https://doi.
org/10.1016/j.bbapap.2015.10.004
164
S. K. Panday and I. Ghosh
Concanavalin A. J Phys Chem B 109:662–670. https://doi.org/10.1021/jp0477912
51. Young T, Abel R, Kim B et al (2007) Motifs for molecular recognition exploiting
hydrophobic enclosure in protein–ligand binding. Proc Natl Acad Sci 104:808–813. https://
doi.org/10.1073/pnas.0610202104
52. Snyder PW, Mecinovic J, Moustakas DT et al (2011) Mechanism of the hydrophobic effect
in the biomolecular recognition of arylsulfonamides by carbonic anhydrase. Proc Natl Acad
Sci 108:17889–17894. https://doi.org/10.1073/pnas.1114107108
53. Sánchez R, Sali A (1997) Advances in comparative protein-structure modelling. Curr Opin
Struct Biol 7:206–214
54. Eswar N, John B, Mirkovic N et al (2003) Tools for comparative protein structure modeling
and analysis. Nucl Acids Res 31:3375–3380
55. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to
check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291.
https://doi.org/10.1107/s0021889892009944
56. Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol
Graph 8:52–6, 29
57. McKinney JD, Zu Bentrup K Höner, Muñoz-Elias EJ et al (2000) Persistence of
Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt
enzyme isocitrate lyase. Nature 406:735–738. https://doi.org/10.1038/35021074
58. Tanjore Soundarajan Balganesh; Santanu Datta; Indira Ghosh (2004) WO2004087943A1
59. Nelson K, Wang FS, Boyd EF, Selander RK (1997) Size and sequence polymorphism in the
isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella
enterica and Escherichia coli. Genetics 147:1509–1520
60. Garnak M, Reeves H (1979) Phosphorylation of isocitrate dehydrogenase of Escherichia
coli. Science 203(80):1111–1112. https://doi.org/10.1126/science.34215
61. Vinekar R, Verma C, Ghosh I (2012) Functional relevance of dynamic properties of dimeric
NADP-dependent isocitrate dehydrogenases. BMC Bioinform 13:S2. https://doi.org/10.
1186/1471-2105-13-s17-s2
62. Vinekar R, Ghosh I (2009) Determination of phosphorylation sites for NADP-specific
isocitrate dehydrogenase from Mycobacterium tuberculosis. J Biomol Struct Dyn 26:741–
754. https://doi.org/10.1080/07391102.2009.10507286
63. Av-Gay Y, Everett M (2000) The eukaryotic-like Ser/Thr protein kinases of Mycobacterium
tuberculosis. Trends Microbiol 8:238–244
64. Hurley JH, Thorsness PE, Ramalingam V et al (1989) Structure of a bacterial enzyme
regulated by phosphorylation, isocitrate dehydrogenase. Proc Natl Acad Sci U S A 86:8635–
8639. https://doi.org/10.1073/pnas.86.22.8635
65. Ceccarelli C, Grodsky NB, Ariyaratne N et al (2002) Crystal structure of porcine
mitochondrial NADP
+ -dependent isocitrate dehydrogenase complexed with Mn
2+ and
isocitrate: Insights into the enzyme mechanism. J Biol Chem 277:43454–43462. https://doi.
org/10.1074/jbc.m207306200
66. Quartararo CE, Hazra S, Hadi T, Blanchard JS (2013) Structural, kinetic and chemical
mechanism of isocitrate dehydrogenase-1 from Mycobacterium tuberculosis. Biochemistry
52:1765–1775. https://doi.org/10.1021/bi400037w
67. Hardin C, Pogorelov TV, Luthey-Schulten Z (2002) Ab initio protein structure prediction.
Curr Opin Struct Biol 12:176–181
68. Bonneau R, Baker D (2001) Ab initio protein structure prediction. Annu Rev Biophys
Biomol Struct 30:173–189
69. Moult J, Fidelis K, Kryshtafovych A et al (2017) Critical assessment of methods of protein
structure prediction (CASP)—round XII. Proteins Struct Funct Bioinform 82:1–6
70. Singh A, Kaushik R, Mishra A et al (2016) ProTSAV: a protein tertiary structure analysis
and validation server. Biochim Biophys Acta Proteins Proteomics 1864:11–19. https://doi.
org/10.1016/j.bbapap.2015.10.004
164
S. K. Panday and I. Ghosh