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Valentin V Rybenkov

TitleProfessor
InstitutionUniversity of Oklahoma, Norman
DepartmentChemistry/Biochemistry
Addressn/a
620 Parrington Oval
Norman OK 73019
Phone405/325-1677
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    Collapse Research 
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    R21AI141927     (RYBENKOV, VALENTIN V)Jul 1, 2019 - Jun 30, 2021
    NIH
    Small molecule inhibitors of bacterial condensins
    Role: Principal Investigator
    R21EY029015     (RYBENKOV, VALENTIN V)Sep 1, 2018 - Aug 31, 2020
    NIH
    Novel Antimicrobials for Eye Infections
    Role: Principal Investigator
    R01AI136799     (GNANAKARAN, SANDRASEGARAM ;RUGGERONE, PAOLO ;RYBENKOV, VALENTIN V;WALKER, JOHN K.;ZGURSKAYA, HELEN I)Feb 7, 2018 - Jan 31, 2024
    NIH
    Optimization of efflux avoidance and inhibition for antibiotic development
    Role: Co-Principal Investigator
    R21AI094124     (RYBENKOV, VALENTIN V)Jul 1, 2011 - Jun 30, 2014
    NIH
    Structural Chromosome Maintenance in Pseudomonas aeruginosa
    Role: Principal Investigator
    R21EB009238     (RYBENKOV, VALENTIN V)Jul 6, 2009 - Jun 30, 2012
    NIH
    Nanomanipulation of analysis of lipoplex assembly
    Role: Principal Investigator
    R01GM063786     (RYBENKOV, VALENTIN V)Aug 1, 2001 - Jul 31, 2006
    NIH
    Mechanism of Bacterial SMC Complex MukBEF
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Manrique PD, Leus IV, L?pez CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S. Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors. Commun Chem. 2024 Apr 12; 7(1):84. PMID: 38609430; PMCID: PMC11015012.
      Citations:    
    2. Hu Z, Leus IV, Chandar B, Sherborne BS, Avila QP, Rybenkov VV, Zgurskaya HI, Duerfeldt AS. Correction to "Structure-Uptake Relationship Studies of Oxazolidinones in Gram-Negative ESKAPE Pathogens". J Med Chem. 2023 Sep 21. PMID: 37733930.
      Citations:    Fields:    
    3. Gervasoni S, Mehla J, Bergen CR, Leus IV, Margiotta E, Malloci G, Bosin A, Vargiu AV, Lomovskaya O, Rybenkov VV, Ruggerone P, Zgurskaya HI. Molecular determinants of avoidance and inhibition of Pseudomonas aeruginosa MexB efflux pump. mBio. 2023 08 31; 14(4):e0140323. PMID: 37493633; PMCID: PMC10470492.
      Citations:    Fields:    Translation:Cells
    4. Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nath D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Author Correction: Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep. 2023 Jun 01; 13(1):8918. PMID: 37264107; PMCID: PMC10235027.
      Citations:    Fields:    
    5. Leus IV, Adamiak J, Chandar B, Bonifay V, Zhao S, Walker SS, Squadroni B, Balibar CJ, Kinarivala N, Standke LC, Voss HU, Tan DS, Rybenkov VV, Zgurskaya HI. Functional Diversity of Gram-Negative Permeability Barriers Reflected in Antibacterial Activities and Intracellular Accumulation of Antibiotics. Antimicrob Agents Chemother. 2023 02 16; 67(2):e0137722. PMID: 36715507; PMCID: PMC9933635.
      Citations: 4     Fields:    Translation:Cells
    6. Manrique PD, L?pez CA, Gnanakaran S, Rybenkov VV, Zgurskaya HI. New understanding of multidrug efflux and permeation in antibiotic resistance, persistence, and heteroresistance. Ann N Y Acad Sci. 2023 01; 1519(1):46-62. PMID: 36344198; PMCID: PMC9839546.
      Citations: 5     Fields:    Translation:HumansCells
    7. Hu Z, Leus IV, Chandar B, Sherborne BS, Avila QP, Rybenkov VV, Zgurskaya HI, Duerfeldt AS. Structure-Uptake Relationship Studies of Oxazolidinones in Gram-Negative ESKAPE Pathogens. J Med Chem. 2022 10 27; 65(20):14144-14179. PMID: 36257060; PMCID: PMC9942527.
      Citations: 5     Fields:    Translation:Cells
    8. Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nash D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep. 2022 05 17; 12(1):8220. PMID: 35581346.
      Citations: 5     Fields:    Translation:HumansCells
    9. Zhao H, Clevenger AL, Coburn PS, Callegan MC, Rybenkov VV. Condensins are essential for Pseudomonas aeruginosa corneal virulence through their control of lifestyle and virulence programs. Mol Microbiol. 2022 04; 117(4):937-957. PMID: 35072315.
      Citations: 1     Fields:    Translation:HumansCells
    10. Sarkar R, Petrushenko ZM, Dawson DS, Rybenkov VV. Ycs4 Subunit of Saccharomyces cerevisiae Condensin Binds DNA and Modulates the Enzyme Turnover. Biochemistry. 2021 11 16; 60(45):3385-3397. PMID: 34723504.
      Citations:    Fields:    Translation:AnimalsCells
    11. D'Cunha N, Moniruzzaman M, Haynes K, Malloci G, Cooper CJ, Margiotta E, Vargiu AV, Uddin MR, Leus IV, Cao F, Parks JM, Rybenkov VV, Ruggerone P, Zgurskaya HI, Walker JK. Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides. ACS Infect Dis. 2021 09 10; 7(9):2650-2665. PMID: 34379382.
      Citations: 6     Fields:    Translation:HumansCells
    12. Rybenkov VV, Zgurskaya HI, Ganguly C, Leus IV, Zhang Z, Moniruzzaman M. The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux. Chem Rev. 2021 05 12; 121(9):5597-5631. PMID: 33596653.
      Citations: 18     Fields:    Translation:HumansCells
    13. Zgurskaya HI, Walker JK, Parks JM, Rybenkov VV. Multidrug Efflux Pumps and the Two-Faced Janus of Substrates and Inhibitors. Acc Chem Res. 2021 02 16; 54(4):930-939. PMID: 33539084.
      Citations: 12     Fields:    Translation:Cells
    14. Mehla J, Malloci G, Mansbach R, López CA, Tsivkovski R, Haynes K, Leus IV, Grindstaff SB, Cascella RH, D'Cunha N, Herndon L, Hengartner NW, Margiotta E, Atzori A, Vargiu AV, Manrique PD, Walker JK, Lomovskaya O, Ruggerone P, Gnanakaran S, Rybenkov VV, Zgurskaya HI. Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa. mBio. 2021 01 19; 12(1). PMID: 33468691.
      Citations: 13     Fields:    Translation:Cells
    15. Zhao H, Bhowmik BK, Petrushenko ZM, Rybenkov VV. Alternating Dynamics of oriC, SMC, and MksBEF in Segregation of Pseudomonas aeruginosa Chromosome. mSphere. 2020 09 09; 5(5). PMID: 32907947.
      Citations: 4     Fields:    Translation:Cells
    16. Mansbach RA, Leus IV, Mehla J, Lopez CA, Walker JK, Rybenkov VV, Hengartner NW, Zgurskaya HI, Gnanakaran S. Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria. J Chem Inf Model. 2020 06 22; 60(6):2838-2847. PMID: 32453589.
      Citations: 15     Fields:    Translation:Cells
    17. Saha P, Sikdar S, Krishnamoorthy G, Zgurskaya HI, Rybenkov VV. Drug Permeation against Efflux by Two Transporters. ACS Infect Dis. 2020 04 10; 6(4):747-758. PMID: 32039579.
      Citations: 16     Fields:    Translation:Cells
    18. Zgurskaya HI, Rybenkov VV. Permeability barriers of Gram-negative pathogens. Ann N Y Acad Sci. 2020 01; 1459(1):5-18. PMID: 31165502.
      Citations: 58     Fields:    Translation:HumansAnimalsCells
    19. Bhowmik BK, Clevenger AL, Zhao H, Rybenkov VV. Segregation but Not Replication of the Pseudomonas aeruginosa Chromosome Terminates at Dif. mBio. 2018 10 23; 9(5). PMID: 30352930.
      Citations: 6     Fields:    Translation:Cells
    20. Zhao H, Petrushenko ZM, Walker JK, Baudry J, Zgurskaya HI, Rybenkov VV. Small Molecule Condensin Inhibitors. ACS Infect Dis. 2018 12 14; 4(12):1737-1745. PMID: 30346684.
      Citations: 8     Fields:    Translation:Cells
    21. Cooper CJ, Krishnamoorthy G, Wolloscheck D, Walker JK, Rybenkov VV, Parks JM, Zgurskaya HI. Molecular Properties That Define the Activities of Antibiotics in Escherichia coli and Pseudomonas aeruginosa. ACS Infect Dis. 2018 08 10; 4(8):1223-1234. PMID: 29756762.
      Citations: 32     Fields:    Translation:Cells
    22. Zgurskaya HI, Rybenkov VV, Krishnamoorthy G, Leus IV. Trans-envelope multidrug efflux pumps of Gram-negative bacteria and their synergism with the outer membrane barrier. Res Microbiol. 2018 Sep - Oct; 169(7-8):351-356. PMID: 29454787.
      Citations: 21     Fields:    Translation:Cells
    23. Krishnamoorthy G, Leus IV, Weeks JW, Wolloscheck D, Rybenkov VV, Zgurskaya HI. Synergy between Active Efflux and Outer Membrane Diffusion Defines Rules of Antibiotic Permeation into Gram-Negative Bacteria. mBio. 2017 10 31; 8(5). PMID: 29089426.
      Citations: 88     Fields:    Translation:HumansCells
    24. Westfall DA, Krishnamoorthy G, Wolloscheck D, Sarkar R, Zgurskaya HI, Rybenkov VV. Bifurcation kinetics of drug uptake by Gram-negative bacteria. PLoS One. 2017; 12(9):e0184671. PMID: 28926596.
      Citations: 37     Fields:    Translation:Cells
    25. Haynes KM, Abdali N, Jhawar V, Zgurskaya HI, Parks JM, Green AT, Baudry J, Rybenkov VV, Smith JC, Walker JK. Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli. J Med Chem. 2017 07 27; 60(14):6205-6219. PMID: 28650638.
      Citations: 25     Fields:    Translation:Cells
    26. Petrushenko ZM, Rybenkov VV. Biochemical Analysis of Bacterial Condensins. Methods Mol Biol. 2017; 1624:145-159. PMID: 28842882.
      Citations: 1     Fields:    Translation:Cells
    27. Sarkar R, Rybenkov VV. Exploring Condensins with Magnetic Tweezers. Methods Mol Biol. 2017; 1624:161-171. PMID: 28842883.
      Citations:    Fields:    Translation:Cells
    28. Krishnamoorthy G, Wolloscheck D, Weeks JW, Croft C, Rybenkov VV, Zgurskaya HI. Breaking the Permeability Barrier of Escherichia coli by Controlled Hyperporination of the Outer Membrane. Antimicrob Agents Chemother. 2016 12; 60(12):7372-7381. PMID: 27697764.
      Citations: 68     Fields:    Translation:Cells
    29. Abdali N, Parks JM, Haynes KM, Chaney JL, Green AT, Wolloscheck D, Walker JK, Rybenkov VV, Baudry J, Smith JC, Zgurskaya HI. Reviving Antibiotics: Efflux Pump Inhibitors That Interact with AcrA, a Membrane Fusion Protein of the AcrAB-TolC Multidrug Efflux Pump. ACS Infect Dis. 2017 01 13; 3(1):89-98. PMID: 27768847.
      Citations: 42     Fields:    Translation:Cells
    30. Zhao H, Clevenger AL, Ritchey JW, Zgurskaya HI, Rybenkov VV. Pseudomonas aeruginosa Condensins Support Opposite Differentiation States. J Bacteriol. 2016 11 01; 198(21):2936-2944. PMID: 27528506.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    31. Rybenkov VV. When Maxwellian demon meets action at a distance: Comment on "Disentangling DNA molecules" by Alexander Vologodskii. Phys Life Rev. 2016 09; 18:150-153. PMID: 27372001.
      Citations: 3     Fields:    Translation:Cells
    32. Petrushenko ZM, Zhao H, Zgurskaya HI, Rybenkov VV. Novobiocin Susceptibility of MukBEF-Deficient Escherichia coli Is Combinatorial with Efflux and Resides in DNA Topoisomerases. Antimicrob Agents Chemother. 2016 05; 60(5):2949-53. PMID: 26926630.
      Citations: 2     Fields:    Translation:Cells
    33. Rybenkov VV, Herrera V, Petrushenko ZM, Zhao H. MukBEF, a chromosomal organizer. J Mol Microbiol Biotechnol. 2014; 24(5-6):371-83. PMID: 25732339.
      Citations: 32     Fields:    Translation:Cells
    34. Rybenkov VV. Maintenance of chromosome structure in Pseudomonas aeruginosa. FEMS Microbiol Lett. 2014 Jul; 356(2):154-65. PMID: 24863732.
      Citations: 4     Fields:    Translation:Cells
    35. Edwards AL, Sangurdekar DP, Jeong KS, Khodursky AB, Rybenkov VV. Transient growth arrest in Escherichia coli induced by chromosome condensation. PLoS One. 2013; 8(12):e84027. PMID: 24376785.
      Citations: 3     Fields:    Translation:Cells
    36. She W, Mordukhova E, Zhao H, Petrushenko ZM, Rybenkov VV. Mutational analysis of MukE reveals its role in focal subcellular localization of MukBEF. Mol Microbiol. 2013 Feb; 87(3):539-52. PMID: 23171168.
      Citations: 12     Fields:    Translation:Cells
    37. Sun Z, Tikhonova EB, Zgurskaya HI, Rybenkov VV. Parallel lipoplex folding pathways revealed using magnetic tweezers. Biomacromolecules. 2012 Oct 08; 13(10):3395-400. PMID: 22988939.
      Citations:    Fields:    
    38. Petrushenko ZM, She W, Rybenkov VV. A new family of bacterial condensins. Mol Microbiol. 2011 Aug; 81(4):881-96. PMID: 21752107.
      Citations: 30     Fields:    Translation:Cells
    39. Petrushenko ZM, Cui Y, She W, Rybenkov VV. Mechanics of DNA bridging by bacterial condensin MukBEF in vitro and in singulo. EMBO J. 2010 Mar 17; 29(6):1126-35. PMID: 20075860.
      Citations: 33     Fields:    Translation:Cells
    40. Vologodskii A, Rybenkov VV. Simulation of DNA catenanes. Phys Chem Chem Phys. 2009 Dec 07; 11(45):10543-52. PMID: 20145800.
      Citations: 5     Fields:    Translation:Cells
    41. Tikhonova EB, Dastidar V, Rybenkov VV, Zgurskaya HI. Kinetic control of TolC recruitment by multidrug efflux complexes. Proc Natl Acad Sci U S A. 2009 Sep 22; 106(38):16416-21. PMID: 19805313.
      Citations: 48     Fields:    Translation:Cells
    42. Rybenkov VV. Towards the architecture of the chromosomal architects. Nat Struct Mol Biol. 2009 Feb; 16(2):104-5. PMID: 19190662.
      Citations: 5     Fields:    Translation:Cells
    43. Cui Y, Petrushenko ZM, Rybenkov VV. MukB acts as a macromolecular clamp in DNA condensation. Nat Struct Mol Biol. 2008 Apr; 15(4):411-8. PMID: 18376412.
      Citations: 50     Fields:    Translation:Cells
    44. She W, Wang Q, Mordukhova EA, Rybenkov VV. MukEF Is required for stable association of MukB with the chromosome. J Bacteriol. 2007 Oct; 189(19):7062-8. PMID: 17644586.
      Citations: 21     Fields:    Translation:Cells
    45. Petrushenko ZM, Lai CH, Rybenkov VV. Antagonistic interactions of kleisins and DNA with bacterial Condensin MukB. J Biol Chem. 2006 Nov 10; 281(45):34208-17. PMID: 16982609.
      Citations: 38     Fields:    Translation:Cells
    46. Wang Q, Mordukhova EA, Edwards AL, Rybenkov VV. Chromosome condensation in the absence of the non-SMC subunits of MukBEF. J Bacteriol. 2006 Jun; 188(12):4431-41. PMID: 16740950.
      Citations: 26     Fields:    Translation:Cells
    47. Petrushenko ZM, Lai CH, Rai R, Rybenkov VV. DNA reshaping by MukB. Right-handed knotting, left-handed supercoiling. J Biol Chem. 2006 Feb 24; 281(8):4606-15. PMID: 16368697.
      Citations: 43     Fields:    Translation:Cells
    48. Dekker NH, Rybenkov VV, Duguet M, Crisona NJ, Cozzarelli NR, Bensimon D, Croquette V. The mechanism of type IA topoisomerases. Proc Natl Acad Sci U S A. 2002 Sep 17; 99(19):12126-31. PMID: 12167668.
      Citations: 54     Fields:    Translation:Cells
    49. Vologodskii AV, Zhang W, Rybenkov VV, Podtelezhnikov AA, Subramanian D, Griffith JD, Cozzarelli NR. Mechanism of topology simplification by type II DNA topoisomerases. Proc Natl Acad Sci U S A. 2001 Mar 13; 98(6):3045-9. PMID: 11248029.
      Citations: 70     Fields:    Translation:Cells
    50. Kimura K, Rybenkov VV, Crisona NJ, Hirano T, Cozzarelli NR. 13S condensin actively reconfigures DNA by introducing global positive writhe: implications for chromosome condensation. Cell. 1999 Jul 23; 98(2):239-48. PMID: 10428035.
      Citations: 136     Fields:    Translation:AnimalsCells
    51. Alexandrov AI, Cozzarelli NR, Holmes VF, Khodursky AB, Peter BJ, Postow L, Rybenkov V, Vologodskii AV. Mechanisms of separation of the complementary strands of DNA during replication. Genetica. 1999; 106(1-2):131-40. PMID: 10710719.
      Citations: 14     Fields:    Translation:Cells
    52. Rybenkov VV, Ullsperger C, Vologodskii AV, Cozzarelli NR. Simplification of DNA topology below equilibrium values by type II topoisomerases. Science. 1997 Aug 01; 277(5326):690-3. PMID: 9235892.
      Citations: 96     Fields:    Translation:HumansAnimalsCells
    53. Rybenkov VV, Vologodskii AV, Cozzarelli NR. The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. Nucleic Acids Res. 1997 Apr 01; 25(7):1412-8. PMID: 9060437.
      Citations: 52     Fields:    Translation:Cells
    54. Rybenkov VV, Vologodskii AV, Cozzarelli NR. The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis. J Mol Biol. 1997 Mar 28; 267(2):299-311. PMID: 9096227.
      Citations: 25     Fields:    Translation:Cells
    55. Rybenkov VV, Vologodskii AV, Cozzarelli NR. The effect of ionic conditions on the conformations of supercoiled DNA. II. Equilibrium catenation. J Mol Biol. 1997 Mar 28; 267(2):312-23. PMID: 9096228.
      Citations: 31     Fields:    Translation:Cells
    56. Rybenkov VV, Cozzarelli NR, Vologodskii AV. Probability of DNA knotting and the effective diameter of the DNA double helix. Proc Natl Acad Sci U S A. 1993 Jun 01; 90(11):5307-11. PMID: 8506378.
      Citations: 107     Fields:    Translation:Cells
    57. Rybenkov VV, Vologodskii AV. [Effective diameter of DNA]. Mol Biol (Mosk). 1992 Nov-Dec; 26(6):1433-9. PMID: 1491684.
      Citations:    Fields:    
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