Wenxiang: a web-server for drawing wenxiang diagrams

Kuo-Chen Chou, Wei-Zhong Lin, Xuan Xiao

.

DOI: 10.4236/ns.2011.310111                

Abstract

The wenxiang diagram was proposed to represent α-helices in a 2D (two dimensional) space (Chou, K.C., Zhang, C.T., Maggiora, G.M. Proteins: Struct., Funct., Genet., 1997, 28, 99-108). It has the capacity to provide more information in a 2D plane about each of the constituent amino acid residues in an α-helix, and is particularly useful for studying and analyzing amphiphilic helices. To meet the increasing requests for getting the program of generating wenxiang diagrams, a user-friendly web-server called “Wenxiang” has been established. It is accessible to the public at the web-site http://www.jci-bioinfo.cn/wenxiang2 or http://icpr.jci.edu.cn/bioinfo/wenxiang2. Further- more, for the convenience of users, here we provide a step-to-step guide for how to use the Wenxiang web-server to generate the desired wenxiang diagrams.

Keywords

Amphiphilic Helix; Helix-Helix Interaction; Hydrophobic; Hydrophilic; 2D Diagram; Wenxiang Diagram; Helical Wheel Diagram

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Richardson, J.S. (1981) The anatomy and taxonomy of protein structure. Advances in Protein Chemistry, 34, 167-339. doi:10.1016/S0065-3233(08)60520-3
[2]	Chou, K.C. (1983) Identification of low-frequency modes in protein molecules. Biochemical Journal, 215, 465-469. PMID 6362659
[3]	Chou, K.C. (1989) Low-frequency resonance and cooperativity of hemoglobin. Trends in Biochemical Sciences, 14, 212. doi:10.1016/0968-0004(89)90026-1
[4]	Martel, P. (1992) Biophysical aspects of neutron scattering from vibrational modes of proteins. Progress in Biophysics and Molecular Biology, 57, 129-179. doi:10.1016/0079-6107(92)90023-Y
[5]	Chou, K.C. (1988) Review: Low-frequency collective motion in biomacromolecules and its biological functions. Biophysical Chemistry, 30, 3-48. doi:10.1016/0301-4622(88)85002-6
[6]	Chou, K.C. and Forsen, S. (1980) Graphical rules for enzyme-catalyzed rate laws. Biochemical Journal, 187, 829-835. PMID 7188428
[7]	Zhou, G.P. and Deng, M.H. (1984) An extension of Chou’s graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways. Biochemical Journal, 222, 169-176. PMID 6477507
[8]	Chou, K.C. (1989) Graphic rules in steady and non- steady enzyme kinetics. Journal of Biological Chemistry, 264, 12074-12079. PMID 2745429
[9]	Andraos, J. (2008) Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: New methods based on directed graphs. Canadian Journal of Chemistry, 86, 342-357. doi:10.1139/v08-020
[10]	Chou, K.C. (1990) Review: Applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems. Biophysical Chemistry, 35, 1-24. doi:10.1016/0301-4622(90)80056-D
[11]	Shen, H.B., Song, J.N. and Chou, K.C. (2009) Prediction of protein folding rates from primary sequence by fusing multiple sequential features. Journal of Biomedical Science and Engineering (JBiSE), 2, 136-143 (openly accessible at http://www.scirp.org/journal/jbise). doi:10.4236/jbise.2009.23024
[12]	Althaus, I.W., Chou, J.J., Gonzales, A.J., Diebel, M.R., Chou, K.C., Kezdy, F.J., Romero, D.L., Aristoff, P.A., Tarpley, W.G. and Reusser, F. (1993) Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E. Journal of Biological Chemistry, 268, 6119-6124. PMID 7681060
[13]	Althaus, I.W., Gonzales, A.J., Chou, J.J., Diebel, M.R., Chou, K.C., Kezdy, F.J., Romero, D.L., Aristoff, P.A., Tarpley, W.G. and Reusser, F. (1993) The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. Journal of Biological Chemistry, 268, 14875-14880. PMID 7686907
[14]	Althaus, I.W., Chou, J.J., Gonzales, A.J., Diebel, M.R., Chou, K.C., Kezdy, F.J., Romero, D.L., Aristoff, P.A., Tarpley, W.G. and Reusser, F. (1993) Kinetic studies with the nonnucleoside HIV-1 reverse transcriptase inhibitor U-88204E. Biochemistry, 32, 6548-6554. doi:10.1021/bi00077a008
[15]	Chou, K.C., Kezdy, F.J. and Reusser, F. (1994) Review: Steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases. Analytical Biochemistry, 221, 217-230. doi:10.1006/abio.1994.1405
[16]	Chou, K.C. (2010) Graphic rule for drug metabolism systems. Current Drug Metabolism, 11, 369-378. doi:10.2174/138920010791514261
[17]	Xiao, X., Wang, P. and Chou, K.C. (2008) Predicting protein structural classes with pseudo amino acid composition: An approach using geometric moments of cellular automaton image. Journal of Theoretical Biology, 254, 691-696. doi:10.1016/j.jtbi.2008.06.016
[18]	Xiao, X., Wang, P. and Chou, K.C. (2009) GPCR-CA: A cellular automaton image approach for predicting G- protein-coupled receptor functional classes. Journal of Computational Chemistry, 30, 1414-1423. doi:10.1002/jcc.21163
[19]	Wu, Z.C., Xiao, X. and Chou, K.C. (2010) 2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids. Journal of Theoretical Biology, 267, 29-34. doi:10.1016/j.jtbi.2010.08.007
[20]	Schiffer, M. and Edmundson, A.B. (1967) Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophysical Journal, 7, 121-135. doi:10.1016/S0006-3495(67)86579-2
[21]	Chou, K.C., Zhang, C.T. and Maggiora, G.M. (1997) Disposition of amphiphilic helices in heteropolar environments. Proteins: Structure, Function, and Genetics, 28, 99-108. doi:10.1002/(SICI)1097-0134(199705)28:1<99::AID-PROT10>3.0.CO;2-C
[22]	Chou, K.C., Nemethy, G. and Scheraga, H.A. (1984) Energetic approach to packing of a-helices: 2. General treatment of nonequivalent and nonregular helices. Jour- nal of American Chemical Society, 106, 3161-3170. doi:10.1021/ja00323a017
[23]	Zhou, G.P. (2011) The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism. Journal of Theoretical Biology, 284, 142-148. doi:10.1016/j.jtbi.2011.06.006
[24]	Zhou, G.P. (2011) The structural determinations of the leucine zipper coiled-coil domains of the cGMP-Dependent protein kinase I alpha and its interaction with the myosin binding subunit of the myosin light chains phosphase. Proteins & Peptide Letters, 18, 966-978. PMID 21592084