aaaaaaaaa Publications » Gregory V. Nikiforovich - Cogito ergo sum
Gregory V. Nikiforovich                   COGITO  ERGO  SUM
HOME
SCIENCE
        About Me
        Research
        Publications
        Papers in Russian
        Collaborations
MolLife Design LLC
NOT SCIENCE (Russian)
        Books
        Essays
LOG: Aug. 13, 2017
PUBLICATIONS

Some data on early monographs in Russian:


The papers are ranged over five-year periods. Most are with PDF files.



2006 - present


2001 - 2005

1996 - 2000

1991 - 1995

Prior 1991


2006 - present
 
80. Nikiforovich GV, Baranski TJ. Structural mechanisms of constitutive activation in the C5a receptors with mutations in the extracellular loops: Molecular modeling study. Proteins: Structure, Function and Bioinformatics, 2012; 80: 71-80 [PDF]

79. Nikiforovich GV, Taylor CM., Marshall, GR, Baranski, TJ. Difference between restoring and predicting 3D structures of the loops in G-protein-coupled receptors by molecular modeling (Letter to Editor, published online) Proc. Natl. Acad. Sci. USA, 2011; doi/10.1073/pnas.1107702108 [PDF]

78. Ye Y, Xu B, Nikiforovich GV, Bloch S, Achilefu S. Exploring new near-infrared fluorescent disulfide-based cyclic RGD peptide analogs for potential integrin-targeted optical imaging. Bioorg. Medicinal Chem. Letters, 2011; 21: 2116-2120 [PDF]

77. Nikiforovich GV, Taylor CM., Marshall, GR, Baranski, TJ. Simplified modeling approach suggests structural mechanisms for constitutive activation of the C5a receptor. Proteins: Structure, Function and Bioinformatics, 2011; 79: 787-802 [PDF]

76. Nikiforovich GV, Baranski TJ. Computational modeling of constitutively active mutants of GPCRs: C5a receptors. Methods in Enzymology, 2010; 485: 369-392 [PDF]

75. Tao Y-X, Huang H, Wang Z-Q, Yang F, Williams JN, Nikiforovich GV. Constitutive activity of neural melanocortin receptors, 2010, Methods in Enzymology, 2010; 484: 267-279 [PDF]

74. Nikiforovich GV, Taylor CM., Marshall, GR, Baranski, TJ. Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors. Proteins: Structure, Function and Bioinformatics, 2010; 78: 271-285 [PDF]

73. Nikiforovich, G.V., T.J. Baranski, Structural models for the complex of chemotaxis inhibitory protein of Staphylococcus aureus with the C5a receptor. Biochem. Biophys. Res. Commun., 2009; 390: 481-484 [PDF]

72. M. Michino, E. Abola, GPGR Dock participants, C. L. Brooks, 3rd, J. S. Dixon, J. Moult, and R. C. Stevens, Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008, Nature Reviews. Drug Discovery 8 (2009) 455-463 [PDF] (C.M. Taylor and me are among co-authors collectively listed in the paper as GPCR Dock participants.)

71. Nikiforovich, G.V. and G.R. Marshall, Computational Approaches in Peptide and Protein Design: An Overview, in Peptide and Protein Design for Biopharmaceutical Applications, K. Jensen, Editor. 2009, John Wiley & Sons: NY.

70. Klco, J. M.; Sen, S.; Hansen, J.L.; Lyngso, C.; Nikiforovich, G. V.; Sheikh, S.P.; Baranski, T. J. Complement factor 5a receptor chimeras reveal the importance of lipid-facing residues in transport competence. FEBS Journal 2009; 276: 2786-2800 [PDF]

69. Hagemann, I. S.; Miller, D.; Klco, J. M.; Nikiforovich, G. V.; Baranski, T. J. Structure of the complement factor 5a (C5a) receptor/ligand complex studied by disulfide trapping and molecular modeling. J. Biol. Chem. 2008; 283: 7763-7775 [PDF]

68. 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]

67. 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]

66. 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]

65. 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]

64. 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]

63. 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]

62. 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]

61. 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]

60. 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]

59. 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]

58. 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]

57. 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]

56. 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]

55. Vĺbenř, 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]

54. Vĺbenř, J, Nikiforovich, GV, Marshall, GR. A minimalistic 3D pharmacophore model for cyclopentapeptide CXCR4 antagonists. Biopolymers, 2006; 84:459-471. [PDF]

53. 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]

52. 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]

51. 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]

50. 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]


[Top]



2001 - 2005

49. 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]

48. 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]

47. Nikiforovich, GV, Marshall, GR. Three-Dimensional model for Meta-II rhodopsin, an activated G-protein-coupled receptor. Biochemistry, 2003; 42:9110-9120. [PDF]

46. 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]

45. 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]

44. 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. [PDF]

43. 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]

42. 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]

41. 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]

40. Nikiforovich GV, Marshall GR. Editorial: Current Developments in Computational Studies of Peptides. Biopolymers (Peptide Science), 2001; 60: 77-78.[Editorial - PDF]

39. 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]

38. 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]


[Top]

1996 - 2000

37. Nikiforovich GV
, Kövér KE, Zhang WJ, Marshall GR. Cyclopentapeptides as Flexible Conformational Templates. J. Am. Chem. Soc. 2000; 122(14):3262-3273. [PDF]

36. 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]

35. Tseitin VM, Nikiforovich GV. Isolated transmembrane helices arranged across a membrane: computational studies. Protein Engineering 1999; 12(4):305-311. [PDF]

34. Nikiforovich GV. A Novel Non-Statistical Method for Predicting Breaks in Transmembrane Helices. Protein Engineering 1998; 11:279-283. [PDF]

33. 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]

32. 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.

31. 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.

30. 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]

29. 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]

28. 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]

27. 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.


[Top]

1991 - 1995

26. Nikiforovich GV
. Towards non-peptide agonists: Design of "true" peptidomimetics. Letters in Peptide Science 1995; 2: 172-176.

25. 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.

24. 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]

23. 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]

22. 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.

21. 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.

20. Nikiforovich GV, Marshall GR. Conformations of angiotensin vs. its nonpeptidic antagonists. Polish J. Chem. 1994; 68:901-905.

19. Nikiforovich GV
. Computational molecular modeling in peptide design. (Review) Int. J. Peptide Protein Res. 1994; 44: 513-531.

18. 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.

17. 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.

16. Nikiforovich GV, Marshall GR. Conformation-Function Relationships in LHRH Analogs. I. Conformations of LHRH, Int. J. Peptide Protein Res. 1993; 42:171-180.

15. 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.

14. 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.

13. Nikiforovich GV, Prakash O, Gehrig CA, Hruby VJ. Conformations of Dermenkephalin Backbone in DMSO Solution, J. Am. Chem. Soc., 1993; 115:3399-3406.

12. 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.

11. Nikiforovich GV, Hruby VJ. Models for A- and B-receptor-bound conformations of CCK-8. Biochem. Biophys. Res. Commun., 1993; 194:9-16.

10. 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.

9. Nikiforovich GV, Hruby VJ, Prakash O, Gehrig CA. Topographical Requirements for Delta-Selective Opioid Peptides. Biopolymers 1991; 31(8):941-955.

8. 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.

7. 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.

6. 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.

5. 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.


[Top]

Prior 1991

4. 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.

3. 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.

2. 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.

1. Nikiforovich GV. Conformation-Function Relationships for Peptide Bioregulators as Revealed by Theoretical Conformational Analysis - J. Mol. Structure (THEOCHEM), 1986, v.134, pp.325-340.


[Top]


Monographs in Russian:








 



  "Diffusion in Complex Molecular 
   Structures
" by S.G. Galaktionov, 
  G.V. Nikiforovich and T.L. Perelman -
  Minsk, 1974.

  The book was roughly based on 
  my Ph.D. thesis. 
























 "Angiotensin: Molecular Mechanisms
 of Action
" by S.G. Galaktionov,
 G.V. Nikiforovich, G.I. Chipens and
 M.D. Shenderovich - Riga, 1979.


 The book summarized our studies on
 structure and function of angiotensin II.






















 

 


"Conformations of Peptide Bioregulators"
 by G.V. Nikiforovich, S.G. Galaktionov and
 G.I. Chipens - Moscow, 1983.


  The book was roughly based on 
  my D.Sc. thesis. 






















[Top]
  Copyright (c)2009 Gregory V. Nikiforovich& MySiteBuilder.com