Summary.
The cleavage property of hemagglutinin (HA) by different proteases was the prime determinant for influenza A virus pathogenicity. In order to understand the cleavage mechanism, molecular modeling tools were utilized to study the coupled model systems of the proteases, i.e., trypsin and furin and peptides of the cleavage sites specific to H5N1 and H1 HAs, which constitute models of HA precursor in complex with cleavage proteases. The peptide segments ‘RERRRKKR ↓ G’ and ‘SIQSR ↓ G’ from the high pathogenic H5N1 H5 and the low pathogenic H1N1 H1 cleavage sites were docking to the trypsin and furin active pockets, respectively. It was observed through the docking studies that trypsin was able to recognize and cleave both the high pathogenic and low pathogenic hemagglutinin, while furin could only cleave the high pathogenic hemagglutinin. An analysis of binding energies indicated that furin got most of its selectivity due to the interactions with P1, P4, and P6, while having less interaction with P2 and little interactions with P3, P5, P7, and P8. Some mutations of H5N1 H5 cleavage sequence fitted less well into furin and would reduce high pathogenicity of the virus. These findings hint that we should focus at the subsites P1, P4, and P6 for developing drugs against H5N1 viruses.
Article PDF
Similar content being viewed by others
References
M Buck S Bouguet-Bonnet RW Pastor AD MacKerell SuffixJr (2006) ArticleTitleImportance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme Biophys J 90 L36–L38 Occurrence Handle16361340 Occurrence Handle10.1529/biophysj.105.078154 Occurrence Handle1:CAS:528:DC%2BD28Xhslaku7c%3D
KC Chou (1993) ArticleTitleA vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins J Biol Chem 268 16938–16948 Occurrence Handle8349584 Occurrence Handle1:CAS:528:DyaK3sXlvFygsbY%3D
KC Chou (1996) ArticleTitleReview: prediction of HIV protease cleavage sites in proteins Anal Biochem 233 1–14 Occurrence Handle8789141 Occurrence Handle10.1006/abio.1996.0001 Occurrence Handle1:CAS:528:DyaK28XmtVKmsA%3D%3D
KC Chou (2004a) ArticleTitleInsights from modelling the 3D structure of the extracellular domain of alpha7 nicotinic acetylcholine receptor Biochem Biophys Res Commun 319 433–438 Occurrence Handle10.1016/j.bbrc.2004.05.016 Occurrence Handle1:CAS:528:DC%2BD2cXkslSjtLg%3D
KC Chou (2004b) ArticleTitleMolecular therapeutic target for type-2 diabetes J Proteome Res 3 1284–1288 Occurrence Handle10.1021/pr049849v Occurrence Handle1:CAS:528:DC%2BD2cXosVOktbs%3D
KC Chou (2004c) ArticleTitleReview: structural bioinformatics and its impact to biomedical science Curr Med Chem 11 2105–2134 Occurrence Handle1:CAS:528:DC%2BD2cXlslWltbw%3D
KC Chou (2005a) ArticleTitleCoupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein J Proteome Res 4 1681–1686 Occurrence Handle10.1021/pr050145a Occurrence Handle1:CAS:528:DC%2BD2MXmsVyitro%3D
KC Chou (2005b) ArticleTitleModeling the tertiary structure of human cathepsin-E Biochem Biophys Res Commun 331 56–60 Occurrence Handle10.1016/j.bbrc.2005.03.123 Occurrence Handle1:CAS:528:DC%2BD2MXjsFChs7k%3D
KC Chou L Carlacci (1991) ArticleTitleSimulated annealing approach to the study of protein structures Protein Eng 4 661–667 Occurrence Handle1946323 Occurrence Handle10.1093/protein/4.6.661 Occurrence Handle1:CAS:528:DyaK3MXlslyrsLw%3D
KC Chou DQ Wei QS Du S Sirois WZ Zhong (2006) ArticleTitleReview: progress in computational approach to drug development against SARS Curr Med Chem 13 3263–3270 Occurrence Handle17168850 Occurrence Handle10.2174/092986706778773077 Occurrence Handle1:CAS:528:DC%2BD28XhtFyrtr%2FL
KC Chou DQ Wei WZ Zhong (2003) ArticleTitleBinding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS Biochem Biophys Res Commun 308 148–151 Occurrence Handle12890493 Occurrence Handle10.1016/S0006-291X(03)01342-1 Occurrence Handle1:CAS:528:DC%2BD3sXlvVCktbk%3D
QS Du H Sun KC Chou (2007a) ArticleTitleInhibitor design for SARS coronavirus main protease based on “distorted key theory” Med Chem 3 1–6 Occurrence Handle10.2174/157340607779317616 Occurrence Handle1:CAS:528:DC%2BD2sXisVyhsrg%3D
QS Du S Wang DQ Wei S Sirois KC Chou (2005) ArticleTitleMolecular modelling and chemical modification for finding peptide inhibitor against SARS CoV Mpro Anal Biochem 337 262–270 Occurrence Handle15691506 Occurrence Handle10.1016/j.ab.2004.10.003 Occurrence Handle1:CAS:528:DC%2BD2MXhtVKiu7k%3D
QS Du SQ Wang KC Chou (2007b) ArticleTitleAnalogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus Biochem Biophys Res Commun 362 525–531 Occurrence Handle10.1016/j.bbrc.2007.08.025 Occurrence Handle1:CAS:528:DC%2BD2sXpvFKmsLw%3D
QS Du SQ Wang DQ Wei Y Zhu H Guo S Sirois KC Chou (2004) ArticleTitlePolyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of octapeptide Peptides 25 1857–1864 Occurrence Handle15501516 Occurrence Handle10.1016/j.peptides.2004.06.018 Occurrence Handle1:CAS:528:DC%2BD2cXovV2gu7k%3D
M Hatta P Gao P Halfmann Y Kawaoka (2001) ArticleTitleMolecular basis for high virulence of Hong Kong H5N1 influenza A viruses Science 293 1840–1842 Occurrence Handle11546875 Occurrence Handle10.1126/science.1062882 Occurrence Handle1:CAS:528:DC%2BD3MXmvVSktrw%3D
S Henrich A Cameron GP Bourenkov R Kiefersauer R Huber I Lindberg W Bode ME Than (2003) ArticleTitleThe crystal structure of the proprotein processing proteinase furin explains its stringent specificity Nat Struct Biol 10 520–526 Occurrence Handle12794637 Occurrence Handle10.1038/nsb941 Occurrence Handle1:CAS:528:DC%2BD3sXkvVentr4%3D
S Henrich I Lindberg W Bode ME Than (2005) ArticleTitleProprotein convertase models based on the crystal structures of furin and kexin: explanation of their specificity J Mol Biol 345 211–227 Occurrence Handle15571716 Occurrence Handle10.1016/j.jmb.2004.10.050 Occurrence Handle1:CAS:528:DC%2BD2cXhtVansb%2FO
T Holyoak CA Kettner GA Petsko RS Fuller D Ringe (2004) ArticleTitleStructural basis for differences in substrate selectivity in Kex2 and furin protein convertases Biochemistry 43 2412–2421 Occurrence Handle14992578 Occurrence Handle10.1021/bi035849h Occurrence Handle1:CAS:528:DC%2BD2cXhtVGiu7g%3D
BS Ibrahim N Shamaladevi V Pattabhi (2004) ArticleTitleTrypsin activity reduced by an autocatalytically produced nonapeptide J Biomol Struct Dyn 21 737–744 Occurrence Handle15106996 Occurrence Handle1:CAS:528:DC%2BD2cXksVyqsLo%3D
Y Kawaoka RG Webster (1988) ArticleTitleSequence requirements for cleavage activation of influenza virus hemagglutinin expressed in mammalian cells Proc Natl Acad Sci USA 85 324–328 Occurrence Handle2829180 Occurrence Handle10.1073/pnas.85.2.324 Occurrence Handle1:CAS:528:DyaL1cXht1Ojsb4%3D
H Kido K Sakai Y Kishino M Tashiro (1993) ArticleTitlePulmonary surfactant is a potential endogenous inhibitor of proteolytic activation of Sendai virus and influenza A virus FEBS Lett 322 115–119 Occurrence Handle8387030 Occurrence Handle10.1016/0014-5793(93)81549-F Occurrence Handle1:CAS:528:DyaK3sXlslymt7g%3D
DJ Krysan NC Rockwell RS Fuller (1999) ArticleTitleQuantitative characterization of furin specificity. Energetics of substrate discrimination using an internally consistent set of hexapeptidyl methylcoumarinamides J Biol Chem 274 23229–23234 Occurrence Handle10438496 Occurrence Handle10.1074/jbc.274.33.23229 Occurrence Handle1:CAS:528:DyaK1MXltlKntLo%3D
W Ma C Tang L Lai (2005) ArticleTitleSpecificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant Biophys J 89 1183–1193 Occurrence Handle15923233 Occurrence Handle10.1529/biophysj.104.057158 Occurrence Handle1:CAS:528:DC%2BD2MXnvVSrsrk%3D
J Martin SA Wharton YP Lin DK Takemoto JJ Skehel DC Wiley DA Steinhauer (1998) ArticleTitleStudies of the binding properties of influenza hemagglutinin receptor-site mutants Virology 241 101–111 Occurrence Handle9454721 Occurrence Handle10.1006/viro.1997.8958 Occurrence Handle1:CAS:528:DyaK1cXnvVensg%3D%3D
GM Morris DS Goodsell R Huey AJ Olson (1996) ArticleTitleDistributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4 J Comput Aided Mol Des 10 293–304 Occurrence Handle8877701 Occurrence Handle10.1007/BF00124499 Occurrence Handle1:CAS:528:DyaK28XlsVOhsL0%3D
ES Radisky JM Lee CJ Lu DE Koshland SuffixJr (2006) ArticleTitleInsights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates Proc Natl Acad Sci USA 103 6835–6840 Occurrence Handle16636277 Occurrence Handle10.1073/pnas.0601910103 Occurrence Handle1:CAS:528:DC%2BD28XkslCks7o%3D
L Rozan DJ Krysan NC Rockwell RS Fuller (2004) ArticleTitlePlasticity of extended subsites facilitates divergent substrate recognition by Kex2 and furin J Biol Chem 279 35656–35663 Occurrence Handle15159396 Occurrence Handle10.1074/jbc.M405362200 Occurrence Handle1:CAS:528:DC%2BD2cXmsl2hsLY%3D
I Schechter A Berger (1967) ArticleTitleOn the size of the active site in protease. I. Papain Biochem Biophys Res Commun 27 157–162 Occurrence Handle6035483 Occurrence Handle10.1016/S0006-291X(67)80055-X Occurrence Handle1:CAS:528:DyaF2sXktVyhsrg%3D
A Schmidt C Jelsch P Ostergaard W Rypniewski VS Lamzin (2003) ArticleTitleTrypsin revisited: crystallography AT (SUB) atomic resolution and quantum chemistry revealing details of catalysis J Biol Chem 278 43357–43362 Occurrence Handle12937176 Occurrence Handle10.1074/jbc.M306944200 Occurrence Handle1:CAS:528:DC%2BD3sXosFSrsrs%3D
S Sirois DQ Wei QS Du KC Chou (2004) ArticleTitleVirtual screening for SARS-CoV protease based on KZ7088 pharmacophore points J Chem Inf Comput Sci 44 1111–1122 Occurrence Handle15154780 Occurrence Handle10.1021/ci034270n Occurrence Handle1:CAS:528:DC%2BD2cXhs1yitLc%3D
DA Steinhauer (1999) ArticleTitleRole of hemagglutinin cleavage for the pathogenicity of influenza virus Virology 258 1–20 Occurrence Handle10329563 Occurrence Handle10.1006/viro.1999.9716 Occurrence Handle1:CAS:528:DyaK1MXivFOqt7s%3D
J Stevens O Blixt TM Tumpey JK Taubenberger JC Paulson IA Wilson (2006) ArticleTitleStructure and receptor specificity of the hemagglutinin from an H5N1 influenza virus Science 312 404–410 Occurrence Handle16543414 Occurrence Handle10.1126/science.1124513 Occurrence Handle1:CAS:528:DC%2BD28XjslSktbY%3D
JF Wang DQ Wei L Li SY Zheng YX Li KC Chou (2007a) ArticleTitle3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design Biochem Biophys Res Commun 355 513–519 Occurrence Handle10.1016/j.bbrc.2007.01.185 Occurrence Handle1:CAS:528:DC%2BD2sXitFOlsbs%3D
SQ Wang QS Du KC Chou (2007b) ArticleTitleStudy of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases Biochem Biophys Res Commun 354 634–640 Occurrence Handle10.1016/j.bbrc.2006.12.235 Occurrence Handle1:CAS:528:DC%2BD2sXhtlOgtbc%3D
SQ Wang QS Du K Zhao AX Li DQ Wei KC Chou (2007c) ArticleTitleVirtual screening for finding natural inhibitor against cathepsin-L for SARS therapy Amino Acids 33 129–135 Occurrence Handle10.1007/s00726-006-0403-1
DQ Wei QS Du H Sun KC Chou (2006a) ArticleTitleInsights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands Biochem Biophys Res Commun 344 1048–1055 Occurrence Handle10.1016/j.bbrc.2006.03.210 Occurrence Handle1:CAS:528:DC%2BD28XktVOqsL4%3D
DQ Wei S Sirois QS Du HR Arias KC Chou (2005) ArticleTitleTheoretical studies of Alzheimer’s disease drug candidate [(2,4-dimethoxy) benzylidene]-anabaseine dihydrochloride (GTS-21) and its derivatives Biochem Biophys Res Commun 338 1059–1064 Occurrence Handle16256952 Occurrence Handle10.1016/j.bbrc.2005.10.047 Occurrence Handle1:CAS:528:DC%2BD2MXht1WjurrJ
DQ Wei R Zhang QS Du WN Gao Y Li H Gao SQ Wang X Zhang AX Li S Sirois KC Chou (2006b) ArticleTitleAnti-SARS drug screening by molecular docking Amino Acids 31 73–80 Occurrence Handle10.1007/s00726-006-0361-7 Occurrence Handle1:CAS:528:DC%2BD28XntVSmsL0%3D
H Wei R Zhang C Wang H Zheng KC Chou DQ Wei (2007) ArticleTitleMolecular insights of SAH enzyme catalysis and their implication for inhibitor design J Theor Biol 244 692–702 Occurrence Handle17069857 Occurrence Handle10.1016/j.jtbi.2006.09.011 Occurrence Handle1:CAS:528:DC%2BD2sXhtVKlsLs%3D
JL Wheatley T Holyoak (2007) ArticleTitleDifferential P1 arginine and lysine recognition in the prototypical proprotein convertase Kex2 Proc Natl Acad Sci USA 104 6626–6631 Occurrence Handle17426142 Occurrence Handle10.1073/pnas.0701983104 Occurrence Handle1:CAS:528:DC%2BD2sXkvFSqu7c%3D
DC Wiley JJ Skehel (1987) ArticleTitleThe structure and function of the hemagglutinin membrane glycoprotein of influenza virus Annu Rev Biochem 56 365–394 Occurrence Handle3304138 Occurrence Handle10.1146/annurev.bi.56.070187.002053 Occurrence Handle1:CAS:528:DyaL2sXltFWiu7k%3D
R Zhang DQ Wei QS Du KC Chou (2006) ArticleTitleMolecular modeling studies of peptide drug candidates against SARS Med Chem 2 309–314 Occurrence Handle16948478 Occurrence Handle10.2174/157340606776930736 Occurrence Handle1:CAS:528:DC%2BD28XmtFSlt7s%3D
Author information
Authors and Affiliations
Additional information
Authors’ address: Dong-Qing Wei, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
Rights and permissions
About this article
Cite this article
Guo, XL., Li, L., Wei, DQ. et al. Cleavage mechanism of the H5N1 hemagglutinin by trypsin and furin. Amino Acids 35, 375–382 (2008). https://doi.org/10.1007/s00726-007-0611-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00726-007-0611-3