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Department of Biochemistry and Molecular Biophysics

Department of Biochemistry & Molecular Biophysics
141 Chalmers Hall
1711 Claflin Rd.
Manhattan, KS 66506
785-532-7278 fax

Biotechnology Core Facility
206 Burt Hall
785-532-6297 fax

Biomolecular NMR Facility
37 Chalmers Hall

Om Prakash, Ph.D., Professor
Director of NMR Facility

Complete publications list

2010s | 2000s | 1990s | 1980s | 1970s | Book chapters and monographs


Herrera, A.; Tomich, J., and Prakash, O. (2016) Membrane Active Peptides. Current Protein and Peptide Science 17 :827-841.

Woehl, J., Takahashi, D., Herrera, A., Geisbrecht, B. and Prakash, O. (2016) Backbone and side-chain 1H, 15N, and 13C resonance assignments of Extracellular Adherence Protein Domain 4. Biomol. NMR Assign. DOI:10.1007/s12104-016-9688-5.

Sukthankar P, Whitaker SK, Garcia M, Herrera A, Boatwright M, Prakash O, and Tomich JM. (2015) Thermally Induced Conformational Transitions in Nascent Branched Amphiphilic Peptide Capsules. Langmuir. 2015 Feb 26. [Epub ahead of print]

Takahashi, D., Hiromasa, Y., Kim, Y., Anbanandam, A., Yao, X., Chang, KO., and Prakash, O. (2013). Structural and dynamics characterization of norovirus protease.  Protein science, 22:347-357.

Huang, H., Herrera, A., Luo, Z., Sun, X., and Prakash, O. (2012) Structural transformation and physical properties of a hydrogel forming peptide studied by NMR, TEM and dynamic rheomter.  Biophysical Journal, 103:979-988.

Chang, A., Takahashi, D., Prakash, O., and Kim, Y. (2012) Characterization and inhibition of norovirus proteases of genogroups I and II using a fluorescence resonance energy transfer assay. Virology, 423:125-133.

Takahashi, D., Kim, Y., Chang, K., Anbanandam, A., and Prakash, O. (2012) Backbone and side-chain 1H, 15N, and 13C resonance assignments of Norwalk virus protease.  Biomol. NMR Assign., 6:19-21.

Takahashi, D., Yamashita, S., Prakash, O., and Nishimoto, E. (2011) Rotational Diffusion Analysis of PEG-Induced Protein Interactions.  J. of Phys. Chem. B., 115:11786-11792.

Bai, Y., Shi, Y., Herrera, AI., and Prakash, O. (2011) Study of octenyl succinic anhydride modified waxy maize starch by nuclear magnetic resonance spectroscopy.  Carbohydrate Polymers, 83:407-413.

Shera, JN., Takahashi, D., Herrera, A., Prakash, O., and Sun, X. (2010) Morphology and Structural Properties of pH-Responsive Amphiphilic Peptides.  Journal of Nanoscience and Nanotechnology, 10:7981-7987.

Takahashi, D., Shukla, SK., Prakash, O., and Zhang, G. (2010) Structural Determinants of Host Defense Peptides for Antimicrobial Activity and Target Cell Selectivity.  Biochimie, 92:1236-1241.

Sang, Y., Seib, P., Herrera, A., Prakash, O., and Shi, Y. (2010) Effects of Alkaline Treatment on Structure of Phosphorylated Wheat Starch and its Digestibility.  Food Chemistry, 118:323-327.

Herrera, AI., Al-Rawi, A., Cook, GA., Gao, J., Iwamoto, T., Prakash, O., Tomich, JM., and Chen, J. (2010) Introduction of a C-Terminal Tryptophan in a Pore-Forming Peptide: A Structure/Activity Study.  Proteins: Structure, Function, and Bioinformatics, 78:2238-2250.

Lauer, J., Banerjee, D., Shanks, D., Dai, H., Gong, YX., Prakash, O., and Takemoto, DJ. (2010) NMR structure/Function Relationship of Peptide Corresponding to the C1B1 region of PKCγ. Protein & Peptide Letters, 17:1-10.

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Xiao, Y., Herrera, A., Soulages, JL., Bommineni, Y., Prakash, O., and Zhang, G. (2009) The central kink region of an α-helical host defense peptide, is critically involved in bacterial killing and endotoxin neutralization.  Journal of Innate Immunity, 1:256-280.

Huang, R., Zhiqiang, L., Dai, H., VanderValde, D., Prakash, O., and Jiang, H. (2007) The solution structure of clip domains from Manduca sexta prophenoloxidase activating proteinase-2. Biochemistry 46:11431-11439.

Lin, D., Shanks, D., Prakash, O., and Takemoto, DJ. (2007) Protein Kinase C gamma mutations in the C1B Domain Cause Caspase-3 apoptosis in Lens Epithelial Cells through Gap Junctions.  Experimental Eye Research, 85:113-122.

Bommineni, Y., Dai, H., Gong, Y., Soulages, JL., Frenando, S., DeSilva, U., Prakash, O., and Zhang, G. (2007) Fowlicidine-3 is an a-helical cationic host defense peptide with potent antibacterial and lipopolysccharide-neutralizing activities.  FEBS Journal, 274:418-428

Sang, Y., Prakash, O., and Seib, P. (2007) Characterization of Phosphorylated Cross-Linked Resistant Starch by 31P Nuclear Magnetic Resonance Spectroscopy.  Carbohydrate Polymers, 67:201-212.

Xiao, Y., Dai, H., Bommineni, YR., Soulages, JL., Gong, YX., Prakash, O., and Zhang, G. (2006) Structure-Activity Relationships of Fowlicidin-1, a Cathelicidin Antimicrobial Peptide in Chicken.  FEBS Journal, 273:2581-2593.

Xiao, Y., Cai, Y., Soulages, JL., Prakash, O., Gilliland, SE., and Zhang, G. (2006) Identification and functional characterization of three chicken cathelicidins with potent antimicrobial activity.  J. Bio. Chem., 281:2858-2867.

Cook, GA., Pajewski, R., Aburi, M., Smith, PE., Prakash, O., Tomich, JM., and Gokel, GW.(2006) NMR Structure and dynamic studies of an anion binding, channel-forming heptapeptide.  J. Am. Chem. Soc., 128:1633-1638.

Sang, Y., Ortega, MT., Blecha, F., Prakash, O., and Melgarejo, T. (2005) Molecular Cloning and Characterization of Three beta-Defensins from Canine Testes. Infection Immunity, 73:2611-2620

Dhanasekaran, M., Baures, PW., VanCompernolle, S., Todd, S., and Prakash, O. (2003) Structural characterization of peptide fragments from hCD81-LEL. Journal of Peptide Research, 61:80-89

Broughman, JR., Shank, LP., Prakash, O., Schultz, BD., Iwamoto, T., Tomich, JM., and Mitchell, K. (2002) Structural Implications of Placing Cationic Residues at either the NH2- or COOH-Terminus in a Pore-forming Synthetic Peptide. The Journal of Membrane Biology, 190(2):93-103

Yu, X-Q., Prakash, O., and Kanost, MR. (2001) Insect ENF Family Peptides With Diverse Biological Activities Display Similar Core Structures in Solution. Medicinal Chemistry Research, 10(7/8):493-501

Tilley, KA., Benjamen, RE., Bagorogoza, KE., Okot-Kotber, BM., Prakash, O., and Kwen, H. (2001) Tyrosine Cross Links: Molecular Basis of Gluten Structure and Function. Journal of Agricultural and Food Chemistry, 49(5):2627-2632

Kirnarsky, L.,  Prakash, O., Vogen, SM., Mitsuharu, N., Hollingsworth, MA., and Sherman, S. (2000) Structural effects of O-glycosylation on a 15-residue peptide from the mucin (MUC1) core protein. Biochemistry, 39(39):12076-12082

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Yu, X-Q., Prakash, O., and Kanost, MR. (1999) Structure of a paralytic peptide from an insect, Manduca sexta. Journal of Peptide Research, 54:256-261

Vogen, SM., Prakash, O., Kirnarsky, L., Sanderson, SD., and Sherman, SA. (1999) Determination of structural elements related to the biological activities of a potent decapeptide agonist of human C5a anaphylatoxin. The Journal of Peptide Research, 54:74-84.

Kirnarsky, L.,  Prakash, O., Vogen, SM., Ikematsu,Y., Johnson-Kaufman, N., Sanderson, SD., Clausen, H., Hollingsworth, MA., and Sherman, S. (1999) Structural analysis of peptide substrates for O-glycosylation. Peptides: Frontiers of Peptide Science.  Eds. James P. Tam and Pravin T.P. Kaumaya, Kluwer Academic publisher, 713-714.

Rajashekar, CB., Zhou, H., Marcum, KB., and Prakash, O. (1999) Glycine betain accumulation and  induction of cold tolerance in strawberry (Fragaria X ananassa Duch.) plants. Plant Science, 148:175-183.

Sherman, S., Kirnarsky, L., Prakash, O., Rogers, HM., Silva,  R.A.G.D., Keiderling, TA.,  Smith, D., Perini, F.,  and Ruddon, RW. (1999) In search of the earliest events of hCGb folding: structural studies of the 60-87 peptide fragment. Peptides: Frontiers of Peptide Science. Eds. James P. Tam and Pravin T.P. Kaumaya, Kluwer Academic publisher, 416-417.

Vogen, SM., Prakash, O., Kirnarsky, L., Sanderson, SD., and Sherman, SA. (1998) NMR analysis of a potent decapeptide agonist of human C5a anaphylatoxin. The Journal of Peptide Research, 51:226-234.

Liu, J., Gong, Y., Prakash, O., Lee, I., Huang, J., and Krishnamoorthi, R. (1998) NMR studiesof internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor (CMTI-III) of the Squash family and comparision with those of counterparts of CMTI-V of the potatoI family. Protein Science,  7:132-141.

Groutas, WC., Kuang, R., Venkataraman, R., Epp, JB., Ruan, S., and Prakash, O. (1997) Structure-based design of a general class of mechanism-based inhibitors of the serine proteinases employing a novel amino acid derived heterocyclic scaffold. Biochemistry, 36:4739-4750.

Groutas, WC., Epp, JB., Venkataraman, R., Kuang, R., Truong, TM., McClenahan, JJ., and Prakash, O., (1996) Design, synthesis and in vitro inhibitory activity toward human leukocyte  elastase, Cathepsin G proteinase 3 of saccharine-derived sulfones and congeners. Biooraganic and Medicinal Chemistry,  4:1393-1400.

Liu, J., Prakash, O., Huang, Y., Wen, L., Wen, J., Huang, JK., and Krishnamoorthi, R. (1996) Internal mobility of reactive-site hydrolyzed recombinant Cucurbita maxima trypsin inhibitor-V characterized by NMR spectroscopy: Evidence for differential stabilization of newly formed C- and N-termini. Biochemistry, 35:12503-12510.

Xu, R., Huang, X., Morgan, TD., Prakash, O., Kramer, KJ., and Hawley, MD. (1996) Characterization of products from the reactions of N-acetyldopamine quinone with N-acetylhistidine. Archives of Biochem. Biophys., 329:56-64.

Cai, M., Huang, Y., Prakash, O., Wen, L., Dunkelbarger, SP., Huang, JK., Liu, J., and   Krishnamoorthi, R. (1996) Differential modulation of binding loop flexibility and stability by  Arg50 and Arg52 in Cucurbita maxima trypsin inhibitor-V deduced by trypsin-catalyzed  hydrolysis and NMR spectroscopy.  Biochemistry, 35:4784-4794.

Vogen, S., Prakash, O., Kirnarsky, L., Sherman, S., Ember, J., Finch, AM., Taylor, SM., and Sanderson, SD. (1996) Conformational requirements for potent decapeptide agonists of  human C5a anaphylatoxin. Peptide: Chemistry, Structure, and Biology, Eds. P.T.P. Kaumaya  & R.S. Hodges, Mayflower Scientific, Ltd., Kingswinford, England, 503-504.

Liu, J., Prakash, O., Cai, M., Gong, Y., Wen, L., Wen, JP., and Krishnamoorthi, R. (1996) Solution structure and backbone dynamics of recombinant Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy. Biochemistry, 35:1516-1524.

Sanderson, SD., Kirnarsky, L., Sherman, SA., Vogen, SA., Prakash, O., Ember, JA., Finch, AM., and Taylor, SM. (1995) Decapeptide agonists of human C5a: The relationship between conformation and neutrophil response. J. Med. Chem., 38:3669-3675.

Cai, M., Gong, Y., Prakash, O., and Krishnamoorthi, R. (1995) Reactive-site Cucurbita maxima trypsin inhibitor-V: Function, thermodynamics stability and NMR solution structure. Biochemistry, 34:12087-12094.

Cai, M., Huang, Y., Prakash, O., Wen, L., Han, SK., and  Krishnamoorthi, R., (1995) Solution conformations and dynamics of arginine side-chains in a protein deduced from and three-bond N15 - H1 coupling constants. J. Magn. Reson., 108:189-191.

Kawamoto, T., Prakash, O., Ostrander, RL., Rheingold, AL., and Borovic, AS. (1995) Metallohelices: Effects of Weak Interactions on Helical Morphology. Inorg. Chem., 34:4294-4295.

Gonnella, NC., Zhang, X., Jin, Y., Prakash, O., Paris, CG., Kolossvary, I., Guida, WC., Bohacek, RS., Vlattas, I., and Sytwu, T. (1994) Solvent effects on the conformation of cyclo(-D-Trp-D-Asp-Pro-D-Val-Leu): An NMR spectroscopy and molecular modelling study. Int. J. of Peptide Protein Res., 43:454-462.

Nikiforovich, GV., Prakash, O., Gehrig, C., and Hruby, VJ. (1993) Solution conformation of the peptide backbone for DPDPE and its b-MePhe4-substituted analogs. Int. J. of Peptide Protein Res., 41:347-361.

Nikiforovich, GV., Prakash, O., Gehrig, C., and Hruby, VJ. (1993) Conformations of the dermenkephalin backbone in DMSO solution by a new approach to the solution conformations of flexible peptides. J. Am. Chem. Soc., 115:3399-3406.

Kover, KE., Prakash, O., and Hruby, VJ. (1993) Z-Filtered heteronuclear coupled HSQC-TOCSY experiments as a means for measuring long range heteronuclear coupling constant. J. Magn. Reson., 103:92-96.

Kover, KE., Prakash, O., and Hruby, VJ. (1993) Improved 2D inverse proton detected C, H-correlation NMR techniques for the total assignment of carbon resonances of a highly delta opioid receptor agonist peptide. Magn. Reson. Chem., 31:231-237.

Kover, KE., Prakash, O., and Hruby, VJ. (1992) Efficient purging sequence for proton detected heteronuclear shift correlation experiments. J. Magn. Reson., 99:426-432.

Gehrig, CA., Toth, G., Prakash, O., and Hruby, VJ. (1991) ?-Me-Phe Containing enkephalin analogues with high selectivity for the delta opioid receptor. Peptide Chemistry, 261-264.

Nikiforovich, GV.,  Hruby, JV., Prakash, O., and Gehrig, CA. (1991) Topographical requirements for delta selective opioid peptides. Biopolymers, 31:941-955.

Agarwal, S., Hussaini, FA., Prakash, O., Roy, R., and Shoeb, A. (1990) Spasmolytic diterpenes from "Pogostemon-Auricularis". Indian J. Chem., 29B:184-186.

Prakash, O., Roy, R., Kapil, RS., and Vishwakarma, RA. (1990) Two-dimensional NMR studies of arteether. Indian J. Chem., 29B:103-107.

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Prakash, O., Roy, R., Bhakuni, DS, Wahidulla, S., and Kamat, SY. (1989) 2D-NMR Studies of a novel steroid from the red alga Acantophora spicifera. J. Natural Products, 52:686-692.

Hruby, VJ., Toth, G., Prakash, O., Davis, P., and Burks, TF. (1988) Cyclic enkephalins which are optically pure isomers of (?Me-p-NO2 Phe )DPDPE possess extraordinary ?-opioid receptor selectivity. Peptides, 616-618.

Prakash, O., Roy, R., Pratap, R., and Bhakuni, DS. (1988) Steric influence on high resolution H-1 NMR spectra of cinchona alkaloids. Indian J. Chem., 27B:950-952.

Prakash, O., Roy, R., Jain, S., and Bhakuni, DS. (1988) The complete assignment of the H-1 and C-13 NMR spectra of isococculidine. J. Natural Products, 51:603-605.

Prakash, O., Roy, R., and Kulshrestha, DK. (1988) Two-dimensional NMR analysis of himachalol and its correlation with other sesquiterpenoids of himachalane series. Magn. Reson. Chem., 26:47-50.

Prakash, O., Roy, R.,  Tandon, JS., and Dhar, MM. (1988) Carbon 13 and Proton Two-dimensional NMR analysis of diterpenoids of Coleus forskohlii. Magn. Reson. Chem., 26:117-119.

Agarwal, S., Prakash, O., Roy, R., Hussaini, FA., and Shoeb, A. (1988) Novel cleistenthane diterpenoid acids from pogostemon auricularis. J. Natural Products, 51:212-216.

Pandey, CB., Prakash, O., Dixit, DK., and Anand, N. (1987) 2-(2-Hydroxynapthalen-2yl)-2-(2,4-dioxo-naptho 1,2b-3,4-dihydro pyran-3-yl) ethylidine: A minor product formed during cyclisation of 2-acetyl napthyl-1 methyl carbonate with potassium carbonate. Indian J. Chem., 26B:1067-1068.

Singh, AK., Lal, K., Prakash, O., Agarwal, AK., and Ray, S. (1987) Facil formation of 9,11-seco estrane-11,17-oxide from corresponding 9.11-seco estranes. Indian J. Chem., 26B:839-842.

Prakash, O., Roy, R., Agarwal, S., Hussaini, FA., and Shoeb, A., (1987) Stereostructure of a cleistanthane diterpenoid using Two-dimensional NMR spectroscopy. Tetrahedron Letters, 28:685-686.

Prakash, O., Roy, R., Garg, HS., and Bhakuni, DS. (1987) C-13 NMR studies of friedelane series of triterpenoids and conformation of D and E rings in friedelan-7one, Magn. Reson. Chem., 25:39-41.

Prakash, O., Roy, R., and Dhar, MM. (1986) A nuclear magnetic resonance study of coleonol. J. Chem. Soc. Perkin, 2:1779-1783.

Sharma, I., Kole, PL., Agarwal, AK., Prakash, O., and Ray, S. (1986) Synthesis and biological activity of 6-aryl estradiol derivatives. Indian J. Chem., 25B:634-637.

Bose, AK., Prakash, O., Hu, GY., and Edasry, J. (1983) Novel use of crown ethers in chemical ionization mass spectroscopy. J. Org. Chem., 48:1780-1782.

Dayal, V., Colman, RW., Prakash, O., Bose, AK., and Sinha, AK. (1983) Cyclic AMP induces synthesis of prostaglandin E1 in platelets. Biochem. Biophys. Acta, 759:129-136.

Bhatia, SK., Prakash, O., and Kapil, RS. (1983) Biosynthesis of codeine using CMR spectroscopy. Indian J. Chem., 20B:701-703.

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Mahesh, VK., Gupta, RS., Sharma, R., and Prakash, O. (1979) Identification of an ?-dipyrane derivative in the synthesis of dehydroactic acid. Ind. J. Chem., 17B:513.

Prakash, O., Bhakuni, DS., and Kapil, RS., (1979) Biosynthesis of coclaurine. J.Chem. Soc. Perkin, 1:1515-1518.

Prakash, O., Bhakuni, DS., Kapil, RS., Rao, GSR., and Ravindranath, B. (1979) Diterpenoids of Roylea calycina (Roxb.). J. Chem. Soc. Perkin, 1:1305-1308.

Prakash, O., Bhakuni DS., and Kapil, RS. (1978) Biosynthesis of Isocorydine (1,2.10-Trimethoxy-6a-aporphine-11-ol). J. Chem. Soc. Perkin, 1:622-624.

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Book chapters and monographs

Zhang, G., Prakash, O., (2010) NMR Insights into Structure-Activity Relationships of Fowlicidins, Chapter 10 in Future Directions of NMR edited by C. L. Khetrapal, Anil Kumar and K.V. Ramanathan, published by Springer-Verlag-India, ISBN: 8184899947.

Prakash, O. and Gulati, A. (1995) Structure-activity relationship of endothelin, In: Endothelin: Role in health and disease, Ed. E. S. Weitenberg, Harwood Academic Publishers, Amsterdam, The Netherlands, 35-51.

Hruby, J. V., Prakash, O., Kazmierski, W. M., Gehrig, C., and Matsunaga, T. O. (1991) Conformational analysis of opioid receptor-selective peptides using NMR and theoretical calculations, Emerging Technologies on Drug Abuse Research, Donna Selig, eds., NIDA Research Monograph 112, 198-217.

Hruby, V. J., Kazmierski, W. M., Matsunaga, T. O., Nikiforovich, G. V., Prakash, O. (1991) Topographical considerations in the design of potent, receptor selective peptide hormones and neuro-transmitters, Expanding Frontiers in Polypeptide and Protein Structural Research, V.Renugopalakrishnan, P.R.Carey, S.G.Yuang, A.Storer and I.C.P.Smith eds., ESCOM Publ. Leiden, The Netherlands.

Gehrig, C., Prakash, O., Toth, G., and Hruby, J. V. (1990) Design and synthesis of opioid receptor selective enkephalin analogues, Problems of Drug Dependence, Louis Harris, ed. NIDIA Research Monograph, 105, 378-379.

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