179
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

Prediction of substrate specificity in NS3/4A serine protease by biased sequence search threading

&
Pages 1102-1114 | Received 12 Jan 2016, Accepted 24 Mar 2016, Published online: 28 Jul 2016

References

  • Akbar, A. , Aydin, C. , Gildemeister, R. , Romano, K. P. , Cao, H. , Özen, A. , … Schiffer, C. A. (2013). Evaluating the role of macrocycles in the susceptibility of hepatitis C virus NS3/4A protease inhibitors to drug resistance. ACS Chemical Biology , 8 , 1469–1478. doi:10.1021/cb400100g
  • Bahar, I. , Atilgan, A. R. , & Erman, B. (1997). Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding and Design , 2 , 173–181. doi:10.1016/S1359-0278(97)00024-2
  • Bahar, I. , & Jernigan, R. L. (1997). Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. Journal of Molecular Biology. , 266 , 195–214. doi:10.1006/jmbi.1996.0758
  • Barkan, D. T. , Hostetter, D. R. , Mahrus, S. , Pieper, U. , Wells, J. A. , Craik, C. S. , & Sali, A. (2010). Prediction of protease substrates using sequence and structure features. Bioinformatics , 26 , 1714–1722. doi:10.1093/bioinformatics/btq267
  • Bartenschlager, R. , Ahlborn-Laake, L. , Yasargil, K. , Mous, J. , & Jacobsen, H. (1995). Substrate determinants for cleavage in cis and in trans by the hepatitis C virus NS3 proteinase. Journal of Virology , 69 , 198–205. Retrieved from http://jvi.asm.org/content/69/1/198.long
  • Chao, L. (2006). HCV NS3-4A serine protease. In Seng-Lai Tan (Ed.), Hepatitis C viruses, genomes and molecular biology (1st ed., pp. 163–206). Indianapolis, IN : Horizon Bioscience.
  • Chen, Y. , & Xu, D. (2003). Computational analyses of high-throughput protein–protein interaction data. Current Protein and Peptide Science , 4 , 159–180. doi:10.1111/0.3466
  • Crooks, G. E. , Hon, G. , Chandonia, J. M. , & Brenner, S. E. (2004). WebLogo: A sequence logo generator. Genome Research , 14 , 1188–1190. doi:10.1101/gr.849004
  • Crooks, G. E. , Wolfe, J. , & Brenner, S. E. (2004). Measurements of protein sequence-structure correlations. Proteins: Structure, Function, and Bioinformatics , 57 , 804–810. doi:10.1002/prot.20262
  • Darden, T. , York, D. , & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics , 98 , 10089–10092. doi:10.1063/1.464397
  • DeLano, W. L. (2002). The PyMOL molecular graphics system . San Carlos, CA: DeLano Scientific.
  • Frecer, V. , Kabeláč, M. , De Nardi, P. , Pricl, S. , & Miertuš, S. (2004). Structure-based design of inhibitors of NS3 serine protease of hepatitis C virus. Journal of Molecular Graphics and Modelling , 22 , 209–220. doi:10.1016/S1093-3263(03)00161-X
  • Funchs, J. E. , Grafenstein, S. V. , Huber, R. G. , Margreiter, M. A. , Spitzer, G. M. , Wallnoefe, H. G. , & Liedl, K. R. (2012). Cleavage entropy as quantitative measure of protease specificity. PLoS Computational Biology , 9 , e1003007. doi:10.1371/journal.pcbi.1003007
  • Goudreau, N. , Cameron, D. R. , Bonneau, P. , Gorys, V. , Plouffe, C. , Poirier, M. , … Llinas-Brunet, M. (2004). NMR structural characterization of peptide inhibitors bound to the hepatitis C virus NS3 protease: design of a new P2 substituent. Journal of Medicinal Chemistry , 47 , 123–132. doi:10.1021/jm0303002
  • Hoffman, N. G. , Schiffer, C. A. , & Swanstrom, R. (2003). Covariation of amino acid positions in HIV-1 protease. Virology , 314 , 536–548. doi:10.1016/S0042-6822(03)00484-7
  • Ingallinella, P. , Altamura, S. , Bianchi, E. , Taliani, M. , Ingenito, R. , Cortese, R. , … Pessi, A. (1998). Potent peptide inhibitors of human hepatitis C virus NS3 protease are obtained by optimizing the cleavage products. Biochemistry , 37 , 8906–8914. doi:10.1021/bi980314n
  • Keskin, O. , & Bahar, I. (1998). Packing of sidechains in low-resolution models for proteins. Folding and Design , 3 , 469–479. doi:10.1016/S1359-0278(98)00064-9
  • Kolykhalov, A. A. , Agapov, E. V. , & Rice, C. M. (1994). Specificity of the hepatitis C virus NS3 serine protease, effects of substitutions at the 3/4A, 4A/4B, 4B/5A and 5A/5B cleavage sites on polyprotein processing. Journal of Virology , 68 , 7525–7533. Retrieved from http://jvi.asm.org/content/68/11/7525.long
  • Kugler, J. , Schmelz, S. , Gentzsch, J. , Haid, S. , Pollmann, E. , Van Den Heuvel, J. , … Collins, J. (2012). High affinity peptide inhibitors of the hepatitis C virus NS3-4A protease refractory to common resistant mutants. Journal of Biological Chemistry , 287 , 39224–39232. doi:10.1074/jbc.M112.393843
  • Kwong, A. D. , McNair, L. , Jacobson, I. , & George, S. (2008). Recent progress in the development of selected hepatitis C virus NS3.4A protease and NS5B polymerase inhibitors. Current Opinion in Pharmacology. , 8 , 522–531. doi:10.1016/j.coph.2008.09.007
  • Landro, J. A. , Raybuck, S. A. , Luong, Y. P. , O’Malley, E. T. , Harbeson, S. L. , Morgenstern, K. A. , … Livingston, D. J. (1997). Mechanistic role of an NS4A peptide cofactor with the truncated NS3 protease of hepatitis C virus: Elucidation of the NS4A stimulatory effect via kinetic analysis and inhibitor mapping. Biochemistry , 36 , 9340–9348. doi:10.1021/bi963054n
  • Leinbach, S. S. , Bhat, R. A. , Xia, S. M. , Hum, W. T. , Stauffer, B. , Davis, A. R. , … Mizutani, S. (1994). Substrate specificity of the NS3 serine proteinase of hepatitis C virus as determined by mutagenesis at the NS3/NS4A junction. Virology , 204 , 163–169. doi:10.1006/viro.1994.1520
  • McClelland, G. H. (1999). Normal probability calculation demonstrations from seeing statistics . Boulder: University of Colorado, Duxbury Press.
  • Meller, J. , & Elber, R. (2001). Linear programming optimization and a double statistical filter for protein threading protocols. Proteins: Structure, Function, and Genetics , 45 , 241–261. doi:10.1002/prot.1145
  • Metropolis, N. , Rosenbluth, A. W. , Rosenbluth, M. N. , Teller, A. H. , & Teller, E. J. (1953). Equation of state calculations by fast computing machines. The Journal of Chemical Physics , 21 , 1087–1092. doi:10.1063/1.1699114
  • Moradpour, D. , & Penin, F. (2013). Hepatitis C virus proteins, from structure to function. Current Topics in Microbiology and Immunology , 369 , 113–142. doi:10.1007/978-3-642-27340-7_5
  • Özen, A. , Sherman, W. , & Schiffer, C. A. (2013). Improving the resistance profile of hepatitis C NS3/4A inhibitors: Dynamic substrate envelope guided design. Journal of Chemical Theory and Computation , 9 , 5693–5705. doi:10.1021/ct400603p
  • Ozer, N. , Haliloglu, T. , & Schiffer, C. A. (2006). Substrate specificity in HIV-1 protease by a biased sequence search method. Proteins: Structure Function and Bioinformatics , 64 , 444–456. doi:10.1002/prot.21023
  • Parera, M. , Martrus, G. , Franco, S. , Clotet, B. , & Martinez, M. A. (2012). Canine hepacivirus NS3 serine protease can cleave the human adaptor proteins MAVS and TRIF. PLoS One , 7 , e42481. doi:10.1371/journal.pone.0042481
  • Phillips, J. C. , Braun, R. , Wang, W. , Gumbart, J. , Tajkhorshid, E. , Villa, E. , … Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry , 26 , 1781–1802. doi:10.1002/jcc.20289
  • Rognvaldsson, T. , Etchells, T. A. , You, L. , Garwicz, D. , Jarman, I. , & Lisboa, P. J. G. (2009). How to find simple and accurate rules for viral protease cleavage specificities. BMC Bioinformatics , 10 , 149–166. doi:10.1186/1471-2105-10-149
  • Romano, K. P. , Ali, A. , Aydin, C. , Soumana, D. , Özen, A. , Deveau, L. M. , … Schiffer, C. A. (2012). The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors. PLoS Pathogens , 8 , e1002832. doi:10.1371/journal.ppat.1002832
  • Romano, K. P. , Ali, A. , Royer, W. E. , & Schiffer, C. A. (2010). Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding. Proceedings of the National Academy of Sciences , 107 , 20986–20991. doi:10.1073/pnas.1006370107
  • Romano, K. P. , Laine, J. M. , Deveau, L. M. , Cao, H. , Massi, F. , & Schiffer, C. A. (2011). Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease. Journal of Virology , 85 , 6106–6116. doi:10.1128/JVI.00377-11
  • Salam, K. A. , & Akimitsu, N. (2013). Hepatitis C virus NS3 inhibitors: Current and future perspectives. BioMed Research International , 2013 , 1–9. Article ID 467869. doi:10.1155/2013/467869
  • Shiryaev, S. A. , Thomsen, E. R. , Cieplak, P. , Chudin, E. , Cheltsov, A. V. , Chee, M. S. , … Strongin, A. Y. (2012). New details of HCV NS3/4A proteinase functionality revealed by a high-throughput cleavage assay. PLoS One , 7 , e35759. doi:10.1371/journal.pone.0035759
  • Tanji, Y. , Hijikata, M. , Hirowatari, Y. , & Shimotohno, K. (1994). Hepatitis C virus polyprotein processing, kinetics and mutagenic analysis of serine proteinase dependent cleavage. Journal of Virology , 68 , 8418–8422. Retrieved from http://jvi.asm.org/content/68/12/8418.long
  • Trellet, M. , Melquiond, A. S. , & Bonvin, A. M. (2013). A unified conformational selection and induced fit approach to protein–peptide docking. PLoS One , 8 , e58769. doi:10.1371/journal.pone.0058769
  • Urbani, A. , Bianchi, E. , Narjes, F. , Tramontano, A. , De Francesco, R. , Steinkuhler, C. , & Pessi, A. (1997). Substrate specificity of the hepatitis C virus serine protease NS3. Journal of Biological Chemistry , 272 , 9204–9209. doi:10.1074/jbc.272.14.9204
  • Venkatraman, S. (2012). Discovery of boceprevir a direct-acting NS3/4A protease inhibitor for treatment of chronic hepatitis C infections. Trends in Pharmacological Sciences , 33 , 289–294. doi:10.1016/j.tips.2012.03.012
  • Webber, C. , & Barton, G. J. (2001). Estimation of P-values for global alignments of protein sequences. Bioinformatics , 17 , 1158–1167. doi:10.1007/978-3-642-27340-7_5
  • Zhang, R. , Durkin, J. , Windsor, W. T. , McNemar, C. & Ramanathan, L. (1997). Probing the substrate specificity of hepatitis C virus NS3 serine protease by using synthetic peptides. Journal of Virology , 71 , 6208–6213. Retrieved from http://jvi.asm.org/content/71/8/6208.long

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.