INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY |
Prev
|
|
|
The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme |
Qi Jian-Xun(齐建勋)a)b) and Jiang Fan(江凡) a)† |
a Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; b Graduate School of the Chinese Academy of Sciences, Beijing 100049, China |
|
|
Abstract The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.
|
Received: 03 December 2010
Revised: 08 January 2011
Accepted manuscript online:
|
PACS:
|
87.15.hp
|
(Conformational changes)
|
|
61.05.C-
|
(X-ray diffraction and scattering)
|
|
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 10674172 and 10874229). |
Cite this article:
Qi Jian-Xun(齐建勋) and Jiang Fan(江凡) The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme 2011 Chin. Phys. B 20 058701
|
[1] |
Gerstein M and Krebs W 1998 Nucleic Acids Res. 26 4280
|
[2] |
Demchenko A P 2001 J. Mol. Recognit. 14 42
|
[3] |
Liu J, Tan H and Rost B 2002 J. Mol. Biol. 322 53
|
[4] |
Palmer A G 2001 Annu. Rev. Biophs. Biomol. Struct. 30 129
|
[5] |
Tainer J A, Getzoff E D, Alexander H, Houghten R A, Olson A J, Lerner R A and Hendrickson W A 1984 Nature 312 127
|
[6] |
Dunker A K, Brown C J, Lawson J D, Iakoucheva L M and Obradovic Z 2002 Biochemistry-Us 41 6573
|
[7] |
Daniel R M, Dunn R V, Finney J L and Smith J C 2003 Annu. Rev. Biophs. Biomol. Struct. 32 69
|
[8] |
Dyson H J and Wright P E 2005 Nat. Rev. Mol. Cell Bio. 6 197
|
[9] |
Tompa P 2005 FEBS Lett. 579 3346
|
[10] |
Dodson G and Verma C S 2006 Cell Mol. Life Sci. 63 207
|
[11] |
Ahmed A, Kazemi S and Gohlke H 2007 Frontiers in Drug Design & Discovery: Structure-Based Drug Design in the 21st Century 3 455
|
[12] |
Das K, Lewi P J, Hughes S H and Arnold E 2005 Prog. Biophys. Mol. Biol. 88 209
|
[13] |
Trueblood K N, Burgi H B, Burzlaff H, Dunitz J D, Gramaccioli C M, Schulz H H, Shmueli U and Abrahams S C 1996 Acta Cryst. A 52 770
|
[14] |
Drenth J 1999 Principles of Protein X-ray Crystallography (New York:Springer Verlag) p81
|
[15] |
Rossmann M G and Arnold E 2006 International Tables for Crystallography (Dordrecht: Kluwer academic publishers) p. 369
|
[16] |
McRee D 1999 Practical Protein Crystallography (New York: Academic) p. 96
|
[17] |
Sternberg M J E, Grace D E P and Phillips D C 1979 J. Mol. Biol. 130 231
|
[18] |
Artymiuk P J, Blake C C F, Grace D E P, Oatley S J, Phillips D C and Sternberg M J E 1979 Nature 280 563
|
[19] |
Karplus P A and Schulz G E 1985 Naturwissenschaften 72 212
|
[20] |
Vihinen M, Torkkila E and Riikonen P 1994 Proteins 19 141
|
[21] |
Smith D K, Radivojac P, Obradovic Z, Dunker A K and Zhu G 2003 Protein Sci. 12 1060
|
[22] |
Schlessinger A and Rost B 2005 Proteins-Structure Function and Bioinformatics 61 115
|
[23] |
Carugo O and Argos P 1998 Proteins-Structure Function and Bioinformatics 31 201
|
[24] |
Yuan Z, Zhao J and Wang Z X 2003 Protein Eng. 16 109
|
[25] |
Vihinen M 1987 Protein Eng. 1 477
|
[26] |
Parthasarathy S and Murthy M R N 2000 Protein Eng. 13 9
|
[27] |
Carugo O and Argos P 1997 Protein Eng. 10 777
|
[28] |
Radivojac P, Obradovic Z, Smith D K, Zhu G, Vucetic S, Brown C J, Lawson J D and Dunker A K 2004 Protein Sci. 13 71
|
[29] |
Kuhs W F 1992 Acta Cryst. A 48 80
|
[30] |
Tronrud D E 1996 J. Appl. Cryst. 29 100
|
[31] |
Tsou C L 1986 Trends Biochem. Sci. 11 427
|
[32] |
Tsou C L 1993 Science 262 380
|
[33] |
Tsou C L 1998 Biochemistry-Moscow 63 253
|
[34] |
Jiang F and Li N 2007 Chin. Phys. 16 392
|
[35] |
Dill K A and Shortle D 1991 Annu. Rev. Biochem. 60 795
|
[36] |
Tanford C 1968 Advan. Prot. Chem. 23 121
|
[37] |
Pike A C W and Acharya K R 1994 Protein Sci. 3 706
|
[38] |
Dunbar J, Yennawar H P, Banerjee S, Luo J B and Farber G K 1997 Protein Sci. 6 1727
|
[39] |
Ratnaparkhi G S and Varadarajan R 1999 Proteins 36 282
|
[40] |
Mande S C and Sobhia M E 2000 Protein Eng. 13 133
|
[41] |
Salem M, Mauguen Y and Prange T 2006 Bba-Proteins Proteom 1764 903
|
[42] |
Otwinowski Z and Minor W 1997 Methods Enzymol. 276 307
|
[43] |
Vagin A and Teplyakov A 1997 J. Appl. Cryst. 30 1022
|
[44] |
Winn M D, Isupov M N and Murshudov G N 2001 Acta Cryst. D 57 122
|
[45] |
Emsley P and Cowtan K 2004 Acta Cryst. D 60 2126
|
[46] |
Adams P D, Grosse-Kunstleve R W, Hung L W, Ioerger T R, McCoy A J, Moriarty N W, Read R J, Sacchettini J C, Sauter N K and Terwilliger T C 2002 Acta Cryst. D 58 1948
|
[47] |
Laskowski R A, Macarthur M W, Moss D S and Thornton J M 1993 J. Appl. Cryst. 26 283
|
[48] |
Dodson E, Winn M and Ralph A 1997 Methods Enzymol. 277 620
|
[49] |
Kleywegt G J 1996 Acta Cryst. D 52 842
|
[50] |
Holm L and Park J 2000 Bioinformatics 16 566
|
[51] |
Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S and Sakaki Y 2000 Proc. Natl. Acad. Sci. 97 1143
|
[52] |
Uetz P, Giot L, Cagney G, Mansfield T A, Judson R S, Knight J R, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S and Rothberg J M 2000 Nature 403 623
|
[53] |
Gavin A C, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick J M, Michon A M, Cruciat C M, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch M, Bastuck S, Huhse B, Leutwein C, Heurtier M A, Copley R R, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G and Superti-Furga G 2002 Nature 415 141
|
[54] |
Ho Y, Gruhler A, Heilbut A, Bader G D, Moore L, Adams S L, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems A R, Sassi H, Nielsen P A, Rasmussen K J, Andersen J R. Johansen L E, Hansen L H, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen, Sorensen B D, Matthiesen J, Hendrickson R C, Gleeson F, Pawson T, Moran M F, Durocher D, Mann M, Hogue C W Figeys D and Tyers M 2002 Nature 415 180
|
[55] |
Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M and Cesareni G 2002 FEBS Lett. 513 135
|
[56] |
Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D and Apweiler R 2004 Nucleic Acids Res. 32 D452
|
[57] |
Tong A H, Evangelista M, Parsons A B, Xu H, Bader G D, Page N, Robinson M, Raghibizadeh S, Hogue C W, Bussey H andrews B, Tyers M and Boone C 2001 Science 294 2364
|
[58] |
Jiang F and Ding W 2010 Chin. Phys. B 19 106101
|
[59] |
Zhang T, Wu L J, Gu Y X, Zheng C D and Fan H F 2010 Chin. Phys. B 19 096101
|
[60] |
Bartlett G J, Porter C T, Borkakoti N and Thornton J M 2002 J. Mol. Biol. 324 105
|
[61] |
Cui Q and Karplus M 2008 Protein Sci. 17 1295
|
[62] |
Schlessinger A, Yachdav G and Rost B 2006 Bioinformatics 22 891 endfootnotesize
|
No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
Altmetric
|
blogs
Facebook pages
Wikipedia page
Google+ users
|
Online attention
Altmetric calculates a score based on the online attention an article receives. Each coloured thread in the circle represents a different type of online attention. The number in the centre is the Altmetric score. Social media and mainstream news media are the main sources that calculate the score. Reference managers such as Mendeley are also tracked but do not contribute to the score. Older articles often score higher because they have had more time to get noticed. To account for this, Altmetric has included the context data for other articles of a similar age.
View more on Altmetrics
|
|
|