Structured crowding and its effects on enzyme catalysis

Topics in Current Chemistry

Volumn 337, Issue , 2013, Pages 123-138

  Ma, Buyong ^a   Nussinov, Ruth ^a,b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

Allostery; Conformational selection; Energy landscape; Enzymatics; Macromolecular crowding; Protein dynamics

Indexed keywords

ENZYME;

ALLOSTERISM; CATALYSIS; CHEMISTRY; PROTEIN CONFORMATION; REVIEW;

ALLOSTERIC REGULATION; CATALYSIS; ENZYMES; PROTEIN CONFORMATION;

EID: 84885977403     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128_2012_316     Document Type: Article

References (110)

1. Ma B, Nussinov R (2010) Curr Opin Chem Biol 14:652
2. Ma B, Kumar S, Tsai CJ, Hu Z, Nussinov R (2000) J Theor Biol 203:383
3. Ansari A, Berendzen J, Bowne SF, Frauenfelder H, Iben IET, Sauke TB, Shyamsunder E, Young RD (1985) Proc Natl Acad Sci USA 82:5000
4. Miller DW, Dill KA (1997) Protein Sci 6:2166
5. Dill KA, Chan HS (1997) Nat Struct Biol 4:10
6. Ohmine I, Tanaka H, Wolynes PG (1988) J Chem Phys 89:5852
7. Ma B, Nussinov R (2009) Proc Natl Acad Sci USA 106:6887
8. de la Cruz L, Nguyen TH, Ozawa K, Shin J, Graham B, Huber T, Otting G (2011) J Am Chem Soc 133:19205
9. Ekonomiuk D, Caflisch A (2009) Protein Sci 18:1003
10. Smith AJ, Muller R, Toscano MD, Kast P, Hellinga HW, Hilvert D, Houk KN (2008) J Am Chem Soc 130:15361
11. Osmulski PA, Hochstrasser M, Gaczynska M (2009) Structure 17:1137
12. Hindie V, Stroba A, Zhang H, Lopez-Garcia LA, Idrissova L, Zeuzem S, Hirschberg D, Schaeffer F, Jorgensen TJ, Engel M, Alzari PM, Biondi RM (2009) Nat Chem Biol 5:758
13. Nussinov R (2012) Mol Biosyst 8:22
14. Konopka MC, Shkel IA, Cayley S, Record MT, Weisshaar JC (2006) J Bacteriol 188:6115
15. Konopka MC, Sochacki KA, Bratton BP, Shkel IA, Record MT, Weisshaar JC (2009) J Bacteriol 191:231
16. Olsen SN, Ramlov H, Westh P (2007) Comp Biochem Physiol A Mol Integr Physiol 148:339
17. Belluzo S, Boeris V, Farruggia B, Pico G (2011) Int J Biol Macromol 49:936
18. Pozdnyakova I, Wittung-Stafshede P (2010) Biochim Biophys Acta 1804:740
19. Pioselli B, Bettati S, Mozzarelli A (2005) FEBS Lett 579:2197
20. Minh DD, Chang CE, Trylska J, Tozzini V, McCammon JA (2006) J Am Chem Soc 128:6006
21. Qin S, Minh DD, McCammon JA, Zhou HX (2010) J Phys Chem Lett 1:107
22. Somalinga BR, Roy RP (2002) J Biol Chem 277:43253
23. Matrai J, Verheyden G, Kruger P, Engelborghs Y (2004) Protein Sci 13:3139
24. Matrai J, Jonckheer A, Joris E, Kruger P, Carpenter E, Tuszynski J, De Maeyer M, Engelborghs Y (2008) Eur Biophys J 38:13
25. Banerjee D, Pal SK (2008) Langmuir 24:8163
26. Sola RJ, Griebenow K (2006) FEBS Lett 580:1685
27. Sola RJ, Griebenow K (2006) FEBS J 273:5303
28. Verma PK, Rakshit S, Mitra RK, Pal SK (2011) Biochimie 93:1424
29. Rodriguez-Martinez JA, Sola RJ, Castillo B, Cintron-Colon HR, Rivera-Rivera I, Barletta G, Griebenow K (2008) Biotechnol Bioeng 101:1142
30. Pastor I, Vilaseca E, Madurga S, Garces JL, Cascante M, Mas F (2011) J Phys Chem B 115: 1115
31. Jordan BJ, Hong R, Han G, Rana S, Rotello VM (2009) Nanotechnology 20:434004
32. Gunasekaran K, Ma B, Nussinov R (2004) Proteins 57:433
33. Lonhienne TG, Winzor DJ (2002) Biochemistry 41:6897
34. del Sol A, Tsai CJ, Ma B, Nussinov R (2009) Structure 17:1042
35. Hiraga K, Derbyshire V, Dansereau JT, Van Roey P, Belfort M (2005) J Mol Biol 354:916
36. Hiraga K, Soga I, Dansereau JT, Pereira B, Derbyshire V, Du Z, Wang C, Van Roey P, Belfort G, Belfort M (2009) J Mol Biol 393:1106
37. Du Z, Liu Y, Ban D, Lopez MM, Belfort M, Wang C (2010) J Mol Biol 400:755
38. Okamoto DN, Oliveira LC, Kondo MY, Cezari MH, Szeltner Z, Juhasz T, Juliano MA, Polgar L, Juliano L, Gouvea IE (2010) Biol Chem 391:1461
39. Wang W, Xu WX, Levy Y, Trizac E, Wolynes PG (2009) Proc Natl Acad Sci USA 106:5517
40. Ercole C, Lopez-Alonso JP, Font J, Ribo M, Vilanova M, Picone D, Laurents DV (2011) Arch Biochem Biophys 506:123
41. Chebotareva NA, Harding SE, Winzor DJ (2001) Eur J Biochem 268:506
42. Chebotareva NA, Kurganov BI, Harding SE, Winzor DJ (2005) Biophys Chem 113:61
43. Chebotareva NA (2007) Biochemistry (Mosc) 72:1478
44. Chebotareva NA, Makeeva VF, Bazhina SG, Eronina TB, Gusev NB, Kurganov BI (2010) Macromol Biosci 10:783
45. Shi J, Han N, Lim L, Lua S, Sivaraman J, Wang L, Mu Y, Song J (2011) PLoS Comput Biol 7:e1001084
46. Jiang M, Guo Z (2007) J Am Chem Soc 129:730
47. Casati DF, Aon MA, Iglesias AA (2000) Biochem J 350(Pt 1):139
48. Moran-Zorzano MT, Viale AM, Munoz FJ, Alonso-Casajus N, Eydallin GG, Zugasti B, Baroja-Fernandez E, Pozueta-Romero J (2007) FEBS Lett 581:1035
49. Li W, Wolynes PG, Takada S (2011) Proc Natl Acad Sci USA 108:3504
50. Brinkman AB, Ettema TJ, de Vos WM, van der Oost J (2003) Mol Microbiol 48:287
51. Ma B, Tsai CJ, Haliloglu T, Nussinov R (2011) Structure 19:907
52. Chen S, Iannolo M, Calvo JM (2005) J Mol Biol 345:251
53. Pul U, Wurm R, Wagner R (2007) J Mol Biol 366:900
54. Ma B, Tsai CJ, Pan Y, Nussinov R (2010) ACS Chem Biol 5:265
55. Sasaki Y, Miyoshi D, Sugimoto N (2007) Nucleic Acids Res 35:4086
56. Santoso Y, Joyce CM, Potapova O, Le Reste L, Hohlbein J, Torella JP, Grindley ND, Kapanidis AN (2010) Proc Natl Acad Sci USA 107:715
57. Andrade P, Martin MJ, Juarez R, Lopez de Saro F, Blanco L (2009) Proc Natl Acad Sci USA 106:16203
58. Eoff RL, Sanchez-Ponce R, Guengerich FP (2009) J Biol Chem 284:21090
59. Xu C, Maxwell BA, Brown JA, Zhang L, Suo Z (2009) PLoS Biol 7:e1000225
60. Rothwell PJ, Waksman G (2007) J Biol Chem 282:28884
61. Simon SM, Sousa FJ, Mohana-Borges R, Walker GC (2008) Proc Natl Acad Sci USA 105: 1152
62. Lareu RR, Harve KS, Raghunath M (2007) Biochem Biophys Res Commun 363:171
63. Sasaki Y, Miyoshi D, Sugimoto N (2006) Biotechnol J 1:440
64. Frueh DP, Arthanari H, Koglin A, Vosburg DA, Bennett AE, Walsh CT, Wagner G (2008) Nature 454:903
65. Guo ZF, Jiang M, Zheng S, Guo Z (2010) Bioorg Med Chem Lett 20:3855
66. Ma B, Kumar S, Tsai CJ, Nussinov R (1999) Protein Eng 12:713
67. Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R (2000) Protein Sci 9:10
68. Ma B, Shatsky M, Wolfson HJ, Nussinov R (2002) Protein Sci 11:184
69. Dong H, Qin S, Zhou HX (2010) PLoS Comput Biol 6:e1000833
70. Cheung MS, Klimov D, Thirumalai D (2005) Proc Natl Acad Sci USA 102:4753
71. Friedel M, Shea JE (2004) J Chem Phys 120:5809
72. Miklos AC, Sarkar M, Wang Y, Pielak GJ (2011) J Am Chem Soc 133:7116
73. Dhar A, Samiotakis A, Ebbinghaus S, Nienhaus L, Homouz D, Gruebele M, Cheung MS (2010) Proc Natl Acad Sci USA 107:17586
74. Miklos AC, Li C, Sorrell CD, Lyon LA, Pielak GJ (2011) BMC Biophys 4:13
75. Homouz D, Perham M, Samiotakis A, Cheung MS, Wittung-Stafshede P (2008) Proc Natl Acad Sci USA 105:11754
76. Bartlett J, Blagojevic J, Carter D, Eskiw C, Fromaget M, Job C, Shamsher M, Trindade IF, Xu M, Cook PR (2006) Biochem Soc Symp 73:67-75
77. Reth M, Wienands J (1997) Annu Rev Immunol 15:453
78. Maudsley S, Martin B, Luttrell LM (2005) J Pharmacol Exp Ther 314:485
79. McGuffee SR, Elcock AH (2010) PLoS Comput Biol 6:e1000694
80. Martorell G, Adrover M, Kelly G, Temussi PA, Pastore A (2011) Proteins 79:1408
81. Szasz CS, Alexa A, Toth K, Rakacs M, Langowski J, Tompa P (2011) Biochemistry 50:5834
82. Li C, Charlton LM, Lakkavaram A, Seagle C, Wang G, Young GB, Macdonald JM, Pielak GJ (2008) J Am Chem Soc 130:6310
83. Derham BK, Harding JJ (2006) Biochim Biophys Acta 1764:1000
84. Ellis RJ (2001) Trends Biochem Sci 26:597
85. Zimmerman SB, Trach SO (1991) J Mol Biol 222:599
86. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) Science 277:1453
87. Pielak GJ (2005) Proc Natl Acad Sci USA 102:5901
88. Minton AP (2006) J Cell Sci 119:2863
89. Zhou HX, Rivas G, Minton AP (2008) Annu Rev Biophys 37:375
90. Minton AP (2001) J Biol Chem 276:10577
91. Dorsaz N, De Michele C, Piazza F, De Los Rios P, Foffi G (2010) Phys Rev Lett 105:120601
92. Zheng Y (2010) Nat Rev Mol Cell Biol 11:529
93. St Johnston D (2005) Nat Rev Mol Cell Biol 6:363
94. Birkenfeld J, Nalbant P, Yoon SH, Bokoch GM (2008) Trends Cell Biol 18:210
95. Good M, Tang G, Singleton J, Remenyi A, Lim WA (2009) Cell 136:1085
96. Seeliger MA, Kuriyan J (2009) Cell 136:994
97. Liu J, Nussinov R (2011) J Biol Chem 286:40934
98. Good MC, Zalatan JG, Lim WA (2011) Science 332:680
99. Csermely P, Palotai R, Nussinov R (2010) Trends Biochem Sci 35:539
100. Di Paolo G, De Camilli P (2006) Nature 443:651
101. Loose M, Kruse K, Schwille P (2011) Annu Rev Biophys 40:315
102. Elcock AH (2010) Curr Opin Struct Biol 20:196
103. Pielak GJ, Miklos AC (2010) Proc Natl Acad Sci USA 107:17457
104. Shaw AK, Pal SK (2007) J Photochem Photobiol B 86:199
105. Hu Z, Bowen D, Southerland WM, del Sol A, Pan Y, Nussinov R, Ma B (2007) PLoS Comput Biol 3:e117
106. Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, Dyson HJ, Benkovic SJ, Wright PE (2011) Science 332:234
107. Agarwal PK, Billeter SR, Rajagopalan PT, Benkovic SJ, Hammes-Schiffer S (2002) Proc Natl Acad Sci USA 99:2794
108. Leventis R, Silvius JR (2010) Biophys J 99:2125
109. Nakano S, Karimata HT, Kitagawa Y, Sugimoto N (2009) J Am Chem Soc 131:16881
110. Xu Y, Wang H, Nussinov R, Ma B (2013) Protein charge and mass contribute to the spatiotemporal dynamics of protein-protein interactions in a minimal proteome. Proteomics. doi:10.1002/pmic.201100540. [Epub ahead of print]