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Nikiforovich G, Marshall, GR, Baranski, TJ. Modeling molecular mechanisms of binding of the anaphylatoxin C5a to the C5a receptor. Biochemistry 2008; 47(10):3117-3130. [PDF]
Sen, S, Baranski, TJ, Nikiforovich G. Conformational movement of F251 contributes to the molecular mechanism of constitutive activation in the C5a receptor. Chemical Biology & Drug Design 2008; 71(3):197-204. [PDF]
Sköld, C, Nikiforovich G, Karlén A. Modeling binding modes of angiotensin II and pseudopeptide analogues to the AT2 receptor. J Mol Graph Model 2008; 26(6):991-1003. [PDF]
Matsumoto, ML, Narzinski, K, Nikiforovich, GV, Baranski, TJ. A Comprehensive structure-function map of the intracellular surface of the human C5a receptor
II. Elucidation of G protein specificity determinants. J. Biol. Chem., 2007; 282(5):3122-3133. [PDF]
Matsumoto, ML, Narzinski, K, Kiser, PD, Nikiforovich, GV, Baranski, TJ. A Comprehensive structure-function map of the intracellular surface of the human C5a receptor
I. Identification of critical residues. J. Biol. Chem., 2007; 282(5):3105-3121. [PDF]
Taylor, CM, Nikiforovich, GV, Marshall, GR. Defining the interface between the C-terminal fragment of α-transducin and photoactivated rhodopsin. Biophys J, 2007; 92:4325-4334. [PDF]
Nikiforovich, GV, Marshall, GR, Achilefu, S. Molecular modeling suggests conformational scaffolds specifically targeting five subtypes of somatostatin receptors. Chemical Biology & Drug Design, 2007; 69(3):163-169. [PDF]
Nikiforovich, GV, Taylor, CM, Marshall, GR. Modeling of the complex between transducin and photoactivated rhodopsin, a prototypical G-protein-coupled receptor. Biochemistry, 2007; 46(16):4734-4744. [PDF]
Zhang, X, Nikiforovich, GV, Marshall, GR. Conformational templates for rational drug design: Flexibility of cyclo(D-Pro1-Ala2-Ala3-Ala4-Ala5) in DMSO solution. J. Med. Chem. 2007; 50(12):2921-2925. [PDF]
Berezin, MY, Lee, H, Akers, W, Nikiforovich, G, Achilefu, S. Ratiometric analysis of fluorescence lifetime for probing binding sites in albumin with near-infrared fluorescent molecular probes. Photochemistry and Photobiology, 2007; 83(6):1371-1378. [PDF]
Klco, JM, Nikiforovich, GV, Baranski, TJ. Genetic analysis of the first and third extracellular loops of the C5a receptor reveals an essential WXFG motif in the first loop. J. Biol. Chem., 2006; 281(17):12010-12019. [PDF]
Nikiforovich, GV, Marshall, GR. 3D modeling of the activated states of constitutively active mutants of rhodopsin. Biochemical and Biophysical Research Communications, 2006; 345(1):430-437. [PDF]
Bloch, S, Xu, B, Ye, Y, Liang, K, Nikiforovich, GV, Achilefu, S. Targeting beta-3 integrin using a linear hexapeptide labeled with a near-infrared fluorescent molecular probe. Mol. Pharmaceutics, 2006; 3(5):539-549. [PDF]
Våbenø, J, Nikiforovich, GV, Marshall, GR. Insight into the binding mode for cyclopentapeptide antagonists of the CXCR4 receptor. Chemical Biology & Drug Design 2006; 67:346-354. [PDF]font>
Våbenø, J, Nikiforovich, GV, Marshall, GR. A minimalistic 3D pharmacophore model for cyclopentapeptide CXCR4 antagonists. Biopolymers, 2006; 84:459-471. [PDF]
Nikiforovich, GV, Zhang, M, Yang, Q, Jagadeesh, G, Chen, H-C, Hunyady, L, Marshall, GR, Catt, KJ. Interactions between Conserved residues in transmembrane helices 2 and 7 during angiotensin AT1 receptor activation. Chemical Biology and Drug Design, 2006; 68:239-249. [PDF]
Hagemann, IS, Nikiforovich, GV, Baranski, TJ. Comparison of the retinitis pigmentosa mutations in rhodopsin with a functional map of the C5a receptor. Vision Research, 2006; 46:4519-4531. [PDF]
Nikiforovich, GV, Zhang, M, Yang, Q, Jagadeesh, G, Chen, HC, Hunyady, L, Marshall, GR, Catt, KJ. Interactions between conserved residues in transmembrane helices 2 and 7 during angiotensin AT1 receptor activation. Chemical Biology & Drug Design, 2006; 68:239-249. [PDF]
Nikiforovich, GV, Marshall, GR. 3D modeling of the activated states of constitutively active mutants of rhodopsin. Biochemical & Biophysical Research Communications, 2006; 345:430-437 . [PDF]
Nikiforovich, GV, Mihalik, B, Catt, KJ, Marshall, GR. Molecular mechanisms of constitutive activity: mutations at position 111 of the angiotensin AT1 receptor. J Peptide Research, 2005; 66:236-248. [PDF]
Nikiforovich, GV, Marshall, GR. Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor. Biophys J, 2005; 89:3780-3789. [PDF]
Nikiforovich, GV, Marshall, GR. Three-Dimensional model for Meta-II rhodopsin, an activated G-protein-coupled
receptor. Biochemistry, 2003; 42:9110-9120. [PDF]
Ye, Y, Li, WP, Anderson, CJ, Kao, GV, Nikiforovich, GV, Achilefu, S. Synthesis and characterization of a macrocyclic near-infrared optical scaffold. J Am Chem Soc, 2003; 125:7766-7767. [PDF]
Nikiforovich
GV. Elements of non-random structure in the unfolded
states of proteins: Location and possible implications for protein
folding mechanisms. Polimery (Warsaw), 2003; 48:44-49. [PDF]
Nikiforovich
GV, Andersen NH, Fesinmeyer RM, Frieden C. Possible Locally
Driven Folding Pathways of TC5b, A 20-Residue Protein. Proteins:
Structure, Function, and Genetics 2003; 52(2):292-302.
Nikiforovich
GV, Frieden C. The search for local
native-like nucleation centers in the unfolded state of Beta-sheet
proteins. Proc. Natl. Acad. Sci. USA 2002; 99(16):10388-10393.
[PDF]
Johanesson
P, Lindeberg G, Johanson A, Nikiforovich GV,
Gogoll A, Synnergren B, Le Greves M, Nyberg F, Karlen A, Hallberg
A. Vinyl Sulfide Cyclized Analogues of Angiotensin
II with High Affinity and Full Agonist Activity at the AT1
Receptor. J. Med. Chem. 2002; 45(9):1767-1777. [PDF]
Nikiforovich
GV, Marshall GR. 3D Model for TM Region of the AT-1
Receptor in Complex with Angiotensin II Independently Validated
by Site-Directed Mutagenesis Data. Biochem. Biophys. Res. Commun.
2001; 286:1204-1211. [PDF]
Galaktionov
S, Nikiforovich GV, Marshall GR. Ab Initio Modeling of
Small, Medium and Large Loops in Proteins. Biopolymers (Peptide
Science) 2001; 60:153-168. [PDF]
Nikiforovich
GV, Galaktionov S, Balodis J, Marshall GR. Novel Approach
to Computer Modeling of Seven-Helical Transmembrane Proteins:
Current Progress in Test Case of Bacteriorhodopsin. Acta Biochimica
Polonica 2001; 44:53-64. [PDF]
Nikiforovich
GV, Kövér KE, Zhang WJ, Marshall GR. Cyclopentapeptides
as Flexible Conformational Templates. J. Am. Chem. Soc. 2000;
122(14):3262-3273. [PDF]
Nikiforovich
GV, Mutter M, Lehmann C. Molecular modeling and design
of regioselectively addressable functionalized templates (RAFT)
with rigidified 3D structures. Biopolymers 1999; 50(4):361-372.
[PDF]
Tseitin VM,
Nikiforovich GV. Isolated transmembrane helices
arranged across a membrane: computational studies. Protein Engineering
1999; 12(4):305-311. [PDF]
Nikiforovich
GV. A Novel Non-Statistical Method for Predicting Breaks
in Transmembrane Helices. Protein Engineering 1998; 11:279-283.
[PDF]
Nikiforovich
GV, Sharma SD, Hadley ME, Hruby VJ. Studies of Conformational
Isomerism in alpha-MSH by Design of Cyclic Analogues. Biopolymers,
1998; 46:155-167. [PDF]
Nikiforovich
GV, Galaktionov SG, Tseitin VM, Lowis DR, Shenderovich
MD, Marshall GR. 3D Modeling for TM Receptors: Algorithms and
Validations. Lett. in Pept. Sci. 1998; 5:413-415.
Flippen-Anderson
JL, Deschamps JR, George C, Nikiforovich GV,
et al. X-ray Structure of Tyr-D-Tic-Phe-Phe-NH2
(D-TIPP-NH2), a Highly Potent mu-Receptor
Selective Opioid Agonist: Comparisons with Proposed Model Structures.
J. Peptide Res. 1997; 49:384-393.
Haskell-Luevano
C, Nikiforovich GV, Sharma SD, et al. Biological
and Conformational Examination of Stereochemical Modifications
Using the Template Melanotropin Peptide, Ac-Nle-c[Asp-His-Phe-Arg-Trp-Ala-Lys]-NH2,
on the Human Melanocortin Receptors. J. Med. Chem. 1997; 40:1738-1748.
[PDF]
Boteju LW, Nikiforovich
GV, Haskell-Luevano C, et al. The Use of Topographical
Constraints In Receptor Mapping: Investigation of the Topographical
Requirements of the Tryptophan 30 Residue for Receptor Binding
of Asp-Tyr-D-Phe-Gly-Trp-(N-Me)Nle-Asp-Phe-NH2
(SNF 9007), a Cholecystokinin (26-33) Analogue That Binds to both
CCK-B and delta-Opioid Receptors. J. Med. Chem. 1996; 39:4120-4124.
[PDF]
Nikiforovich
GV, Kövér KE, Kolodziej SA, et al. Design
and Comprehensive Conformational Studies of Tyr(1)-Cyclo(D-Pen(2)-Gly(3)-Phe(4)-L-3-Mpt(5))
and Tyr(1)-Cyclo(D-Pen(2)-Gly(3)-Phe(4)-D-3-Mpt(5)), Novel Conformationally
Constrained Opioid Peptides. J. Am. Chem. Soc. 1996; 118:959-969.
[PDF]
Shenderovich
MD, Kover KE, Nikiforovich GV, Jiao D, Hruby
VJ. Conformational Analysis of Beta-Methylphenylalanine Stereoisomers
of DPDPE using NMR Data and Conformational Energy Calculations.
Nikiforovich
GV. Towards non-peptide agonists: Design of "true"
peptidomimetics. Letters in Peptide Science 1995; 2: 172-176.
Vakser IA, Nikiforovich
GV. Protein docking in the absence of detailed molecular
structures. In: Atassi MZ, ed. Methods in Protein Structure Analysis.
New York: Plenum Press, 1995; 505-514.
Haskell-Luevano
C, Shenderovich MD, Sharma SD, Nikiforovich GV,
Hadley ME, Hruby VJ. Design, Synthesis, Biology and Conformations
of Bicyclic alpha-Melanotropin Analogues. J. Med. Chem. 1995;
38:1736-1750. [PDF]
Kolodziej
SA, Nikiforovich GV, Skeean R, Lignon M-F, Martinez
J, Marshall GR. Acetyl-(3- and 4-alkylthiolprolyl31)-CCK4 analogs:
synthesis and implications for the CCK-B receptor-bound conformation.
J. Med. Chem. 1995; 38:137-149. [PDF]
Nikiforovich
GV, Kolodziej SA, Nock B, Bernad N, Martinez J, Marshall
GR. Conformationally Readdressed CCK-B/delta-Opioid Peptide Ligands.
Biopolymers 1995; 36:439-452.
Nikiforovich
GV, Marshall GR. Conformations of angiotensin vs. its
nonpeptidic antagonists. Polish J. Chem. 1994; 68:901-905.
Nikiforovich
GV, Kao JL-F, Plucinska K, Zhang WJ, Marshall GR. Conformational
Analysis of Two Cyclic Analogs of Angiotensin: Implications for
the Biologically Active Conformation. Biochemistry 1994; 33:3591-3598.
Stierandova
A, Sepetov NF, Nikiforovich GV, Lebl M. Sequence-dependent
modification of Trp by the Pmc protecting group of Arg during
TFA deprotection. Int. J. Peptide Protein Res. 1994; 43:31-38.
Nikiforovich
GV, Marshall GR. Conformation-Function Relationships
in LHRH Analogs. I. Conformations of LHRH, Int. J. Peptide Protein
Res. 1993; 42:171-180.
Nikiforovich
GV, Marshall GR. Conformation-Function Relationships
in LHRH Analogs. II. Conformations of LHRH peptide agonists and
antagonists, Int. J. Peptide Protein Res.,1993; 42:181-193.
Nikiforovich
GV, Marshall GR. Three-dimensional recognition requirements
for angiotensin agonists: A novel solution for an old problem.
Biochem. Biophys. Res. Commun. 1993; 195(1):222-228.
Nikiforovich
GV, Prakash O, Gehrig CA, Hruby VJ. Conformations of
Dermenkephalin Backbone in DMSO Solution, J. Am. Chem. Soc., 1993;
115:3399-3406.
Nikiforovich
GV, Prakash O, Gehrig C, Hruby VJ. Solution Conformations
of Peptide Backbone for DPDPE and Its Beta-Me-Phe Substituted
Analogs, Int. J. Peptide Protein Res.,1993; 41:347-361.
Nikiforovich
GV, Hruby VJ. Models for A- and B-receptor-bound conformations
of CCK-8. Biochem. Biophys. Res. Commun., 1993; 194:9-16.
Misicka
A, Nikiforovich GV, Lipkowski AW, et al. Topographical
requirements for Delta-opioid ligands: the synthesis and biological
properties of cyclic analog of deltorphin I. Bioorg. and Medicinal
Chemistry Letters, 1992; 2:547-552.
Nikiforovich
GV, Hruby VJ, Prakash O, Gehrig CA. Topographical Requirements
for Delta-Selective Opioid Peptides. Biopolymers 1991; 31(8):941-955.
Vesterman B,
Bobrowski K, Betins J, Nikiforovich GV, Wierzchowski
KL. Conformational interpretation of intramolecular electron transfer
in Met5-enkephalins between Tyr and Met
(S:.Br) radical. Biochimica et Biophysica Acta 1991; 1079:39-42.
Shenderovich
MD, Kasprzykowski F, Liwo A, Sekacis I, Saulitis J, Nikiforovich
GV. Conformational analysis of [Cpp1,Sar7,Arg8]-vasopressin
by 1H-NMR spectroscopy and molecular mechanics
calculations. Int. J. Peptide Protein Res. 1991; 38(6):528-538.
Shenderovich
MD, Nikiforovich GV, Golbraikh AA. Conformational
features responsible for binding of cyclic analogues of enkephalin
to opioid receptors. III. Probable binding conformations of mu-agonists
with phenylalanine in position 3. Int. J. Peptide Protein Res.
1991; 37:241-251.
Nikiforovich
GV, Hruby VJ. Examination of the Conformational Meaning
of "Delta-Address" in the Dermenkephalin Sequence. Biochim.
Biophys. Res. Commun. 1990; 173(2):521-527.
Nikiforovich
GV, Golbraikh AA, Shenderovich MD, Balodis J. Conformational
features responsible for binding of cyclic analogues of enkephalin
to opioid receptors. II. Models of mu- and delta-receptor-bound
structures for analogues containing Phe 4. Int. J. Peptide Protein
Res. 1990; 37:1-12.
Nikiforovich
GV, Balodis J, Shenderovich MD, Golbraikh AA. Conformational
features responsible for binding of cyclic analogues of enkephalin
to opioid receptors. I. Low-energy peptide backbone conformers
of analogues containing Phe 4. Int. J. Peptide
Protein Res. 1990; 36:67-78.
Nikiforovich
GV. Computational molecular modeling in peptide design.
(Review) Int. J. Peptide Protein Res. 1994; 44: 513-531.
Marshall GR, Beusen DD, Nikiforovich GV. Peptide
Conformation - Stability and Dynamics. In: Gutte B, ed. Peptides:
Synthesis, Structures, and Applications. Academic Press, San Diego,
1995, pp. 193-245.
Hruby VJ, Nikiforovich GV. The Ramachandran Plot
and Beyond: Conformational and Topographical Considerations in
the Design of Peptides and Proteins - In: Molecular Conformation
and Biological Interactions, Eds. P. Balaram and S. Ramaseshan,
Indian Academy of Sciences, Bangalore, India, 1991, pp. 429-445.
Nikiforovich GV. Conformation-Function Relationships
for Peptide Bioregulators as Revealed by Theoretical Conformational
Analysis - J. Mol. Structure (THEOCHEM), 1986, v.134, pp.325-340.
Nikiforovich GV, Galaktionov S, Balodis J, Marshall
GR. Novel approach to computer modeling of seven-helical transmembrane
proteins: Current progress in the test case of bacteriorhodopsin.
Acta Biochimica Polonica, 2001; 44: 53-64.
Galaktionov S, Nikiforovich GV, Marshall GR.
Ab initio modeling of small, medium and large loops in proteins.
Biopolymers (Peptide Science), 2001; 60: 153-168.
Nikiforovich GV, Marshall GR. Editorial: Current
Developments in Computational Studies of Peptides. Biopolymers
(Peptide Science), 2001; 60: 77-78.
Nikiforovich GV. Elements of non-random structure
in the unfolded states of proteins: Location and possible implications
for protein folding mechanisms. Polimery, 2003; 48:44-49.
Invited
Lectures (1990 to Present)
1990
Department of Chemistry, University
of California, San Diego. "Biologically Active Conformations
of Opioid Peptides by Energy Calculations".
Department of Biomathematics, Mount Sinai Medical
Center, New York. "Solution Conformations of Oligopeptides:
A New Approach".
Physical & Structural Chemistry, Smith Kline Beecham,
King of Prussia. “Conformational Energy Calculations
in Peptide Drug-Design".
BIOSYM Technologies, San Diego. "Solution Conformations
of Oligopeptides: A New Approach".
Department of Chemistry, University of Louisville, Louisville.
"Conformational Energy Calculations in Peptide Drug-Design".
Bristoll-Mayer-Squibbs, Wallingford. "Conformational
Energy Calculations in Peptide Drug-Design".
1992
Universite Rene Descartes,
Paris, France. "Conformational Factors in Receptor Selectivity
of Peptides: CCK-8 and Opioid Peptides".
CCIPE-Faculte de Pharmacie, Montpellier, France. "Conformational
Factors in Receptor Selectivity of Peptides: CCK-8 and Opioid
Peptides".
Departement Forschung, Kantonsspital Basel, Basel, Switzerland.
"Conformational Isomerism in alpha-MSH Cyclic Analogs".
Centro di Studio sui Biopolimeri, Padova, Italy. "Solution
Conformations of Short Peptides by Combined Use of NMR and Energy
Calculations".
Dipartimento di Chimica, Universita di Napoli Federico II,
Naples, Italy. "Solution Conformations of Short Peptides
by Combined Use of NMR and Energy Calculations".
1993
School of Chemistry, Tel-Aviv University, Tel-Aviv, Israel.
"Molecular Modeling in Biologically Active Peptides".
Workshop on Molecular Modeling, Thirteenth American Peptide
Symposium, Edmonton, Canada. "Peptide Design Based on
Biologically Active Conformation"
Institute of Chemistry, Gdansk University, Gdansk, Poland.
"Technology of Peptide Drug-Design".
1994
A. Menarini Pharmaceuticals, Pomezia (Rome), Italy. "Technology
of Peptide Drug-Design".
Department of Chemistry, University of Louisville, Louisville.
"Computational Technology for Peptide Drug Design".
School of Engineering, Boston University, Boston. "Computational
Technology for Peptide Drug Design".
1995
IBC's Peptidomimetic & Small Molecule Design Conference,
Philadelphia. "Computational Design of "True" Peptidomimetics
Based on Peptide Modeling".
Workshop on Peptidomimetics, Fourteenth American Peptide Symposium,
Columbus. "Conformational Re-Addressing of Peptides
Towards Interactions with Other Specific Receptors".
Symposium on Peptidomimetics, Spa, Belgium. "Towards
Non-Peptide Agonists: Design of "True" Peptidomimetics".
Universite Rene Descartes, Paris, France. "Towards
Non-Peptide Agonists: Design of "True" Peptidomimetics".
Symposium Pharmaco-Clinique Roussel Uclaf, France. "Re-Inventing
The Wheel: Towards "True" Opioid Peptidomimetics".
1996
Astra-Laval, Montreal, Quebec. "3D Models of Delta-Opioid
Agonist Pharmacophore: Approaches, Validation, Design".
1997
Trega Biosciences, San Diego. "Development of alpha-MSH
Pharmacophore".
1998
Axiom Biotechnologies, San Diego. "Design of True
Peptidomimetics out of Peptides".
1998
A. Menarini Pharmaceuticals, Florence, Italy. "Cyclopentapeptides
as Receptor Probes".
1999
University of Nebraska, Omaha. "Cyclopentapeptides
as Receptor Probes".
2000
Kansas State University, Manhattan. "Cyclopentapeptides
as Receptor Probes".
Institute of Organic Chemistry and Biochemistry, Prague, Czech
Republic. “3D Modeling of G-protein Coupled Receptors”.
2001
Summer School on Parallel Computing in Biomolecular Simulations,
Gdansk, Poland. “Restoring small, medium and large
(up to 60 residues) loops in proteins”.
University of Uppsala, Uppsala, Sweden. - “3D Modeling
of G-protein Coupled Receptors”.
2002
Institute for Protein Research, Puschino, Russia. “Elements
of regular structure in unfolded states of proteins”
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow,
Russia. “3D Modeling of G-protein Coupled Receptors”.
