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Items: 29

1.

Structural Adaptation of Darunavir Analogs Against Primary Mutations in HIV-1 Protease.

Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Ali A, Kurt Yilmaz N, Schiffer CA.

ACS Infect Dis. 2018 Dec 13. doi: 10.1021/acsinfecdis.8b00336. [Epub ahead of print]

PMID:
30543749
2.

Structural analysis of the active site and DNA binding of human cytidine deaminase APOBEC3B.

Hou S, Silvas T, Leidner F, Nalivaika EA, Matsuo H, Kurt Yilmaz N, Schiffer CA.

J Chem Theory Comput. 2018 Nov 20. doi: 10.1021/acs.jctc.8b00545. [Epub ahead of print]

PMID:
30457868
3.

HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites.

Potempa M, Lee SK, Kurt Yilmaz N, Nalivaika EA, Rogers A, Spielvogel E, Carter CW Jr, Schiffer CA, Swanstrom R.

J Mol Biol. 2018 Dec 7;430(24):5182-5195. doi: 10.1016/j.jmb.2018.10.022. Epub 2018 Nov 7.

PMID:
30414407
4.

Mutations in Influenza A Virus Neuraminidase and Hemagglutinin Confer Resistance against a Broadly Neutralizing Hemagglutinin Stem Antibody.

Prachanronarong KL, Canale AS, Liu P, Somasundaran M, Hou S, Poh YP, Han T, Zhu Q, Renzette N, Zeldovich KB, Kowalik TF, Kurt-Yilmaz N, Jensen JD, Bolon DNA, Marasco WA, Finberg RW, Schiffer CA, Wang JP.

J Virol. 2019 Jan 4;93(2). pii: e01639-18. doi: 10.1128/JVI.01639-18. Print 2019 Jan 15.

PMID:
30381484
5.

Quinoxaline-Based Linear HCV NS3/4A Protease Inhibitors Exhibit Potent Activity against Drug Resistant Variants.

Rusere LN, Matthew AN, Lockbaum GJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A.

ACS Med Chem Lett. 2018 May 17;9(7):691-696. doi: 10.1021/acsmedchemlett.8b00150. eCollection 2018 Jul 12.

PMID:
30034602
6.

T cell epitope engineering: an avian H7N9 influenza vaccine strategy for pandemic preparedness and response.

Moise L, M Biron B, Boyle CM, Kurt Yilmaz N, Jang H, Schiffer C, M Ross T, Martin WD, De Groot AS.

Hum Vaccin Immunother. 2018;14(9):2203-2207. doi: 10.1080/21645515.2018.1495303. Epub 2018 Sep 5.

7.

Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions.

Silvas TV, Hou S, Myint W, Nalivaika E, Somasundaran M, Kelch BA, Matsuo H, Kurt Yilmaz N, Schiffer CA.

Sci Rep. 2018 May 14;8(1):7511. doi: 10.1038/s41598-018-25881-z.

8.

Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease.

Leidner F, Kurt Yilmaz N, Paulsen J, Muller YA, Schiffer CA.

J Chem Theory Comput. 2018 May 8;14(5):2784-2796. doi: 10.1021/acs.jctc.8b00097. Epub 2018 Apr 18.

PMID:
29570286
9.

Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance.

Khan SN, Persons JD, Paulsen JL, Guerrero M, Schiffer CA, Kurt-Yilmaz N, Ishima R.

Biochemistry. 2018 Mar 13;57(10):1652-1662. doi: 10.1021/acs.biochem.7b01238. Epub 2018 Feb 19.

PMID:
29457713
10.

Structural Determination of the Broadly Reactive Anti-IGHV1-69 Anti-idiotypic Antibody G6 and Its Idiotope.

Avnir Y, Prachanronarong KL, Zhang Z, Hou S, Peterson EC, Sui J, Zayed H, Kurella VB, McGuire AT, Stamatatos L, Hilbert BJ, Bohn MF, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Goodall M, Jefferis R, Zhu Q, Kurt Yilmaz N, Schiffer CA, Marasco WA.

Cell Rep. 2017 Dec 12;21(11):3243-3255. doi: 10.1016/j.celrep.2017.11.056.

11.

Mavyret: A Pan-Genotypic Combination Therapy for the Treatment of Hepatitis C InfectionPublished as part of the Biochemistry series "Biochemistry to Bedside".

Matthew AN, Kurt Yilmaz N, Schiffer CA.

Biochemistry. 2018 Feb 6;57(5):481-482. doi: 10.1021/acs.biochem.7b01160. Epub 2017 Dec 1. No abstract available.

PMID:
29192768
12.

Elucidating the Interdependence of Drug Resistance from Combinations of Mutations.

Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt-Yilmaz N, Schiffer CA.

J Chem Theory Comput. 2017 Nov 14;13(11):5671-5682. doi: 10.1021/acs.jctc.7b00601. Epub 2017 Oct 9.

13.

Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants.

Matthew AN, Zephyr J, Hill CJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt-Yilmaz N, Schiffer CA, Ali A.

J Med Chem. 2017 Jul 13;60(13):5699-5716. doi: 10.1021/acs.jmedchem.7b00426. Epub 2017 Jun 19.

14.

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.

Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn MF, Kelch BA, Royer WE, Somasundaran M, Kurt Yilmaz N, Matsuo H, Schiffer CA.

Nat Commun. 2017 Apr 28;8:15024. doi: 10.1038/ncomms15024.

15.

Interdependence of Inhibitor Recognition in HIV-1 Protease.

Paulsen JL, Leidner F, Ragland DA, Kurt Yilmaz N, Schiffer CA.

J Chem Theory Comput. 2017 May 9;13(5):2300-2309. doi: 10.1021/acs.jctc.6b01262. Epub 2017 Apr 11.

16.

Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side.

Lin KH, Ali A, Rusere L, Soumana DI, Kurt Yilmaz N, Schiffer CA.

J Virol. 2017 Apr 28;91(10). pii: e00045-17. doi: 10.1128/JVI.00045-17. Print 2017 May 15.

17.

Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase.

Prachanronarong KL, Özen A, Thayer KM, Yilmaz LS, Zeldovich KB, Bolon DN, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Kurt-Yilmaz N, Schiffer CA.

J Chem Theory Comput. 2016 Dec 13;12(12):6098-6108. Epub 2016 Nov 17.

PMID:
27951676
18.

Structural and molecular analysis of a protective epitope of Lyme disease antigen OspA and antibody interactions.

Shandilya S, Kurt Yilmaz N, Sadowski A, Monir E, Schiller ZA, Thomas WD Jr, Klempner MS, Schiffer CA, Wang Y.

J Mol Recognit. 2017 May;30(5). doi: 10.1002/jmr.2595. Epub 2016 Nov 16.

19.

Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease.

Soumana DI, Kurt Yilmaz N, Ali A, Prachanronarong KL, Schiffer CA.

J Am Chem Soc. 2016 Sep 14;138(36):11850-9. doi: 10.1021/jacs.6b06454. Epub 2016 Sep 2.

20.

Improving Viral Protease Inhibitors to Counter Drug Resistance.

Kurt Yilmaz N, Swanstrom R, Schiffer CA.

Trends Microbiol. 2016 Jul;24(7):547-557. doi: 10.1016/j.tim.2016.03.010. Epub 2016 Apr 15. Review.

21.

Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172.

Soumana DI, Kurt Yilmaz N, Prachanronarong KL, Aydin C, Ali A, Schiffer CA.

ACS Chem Biol. 2016 Apr 15;11(4):900-9. doi: 10.1021/acschembio.5b00647. Epub 2016 Jan 6.

22.

The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization.

Bohn MF, Shandilya SMD, Silvas TV, Nalivaika EA, Kouno T, Kelch BA, Ryder SP, Kurt-Yilmaz N, Somasundaran M, Schiffer CA.

Structure. 2015 May 5;23(5):903-911. doi: 10.1016/j.str.2015.03.016. Epub 2015 Apr 23.

23.

Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease.

Özen A, Lin KH, Kurt Yilmaz N, Schiffer CA.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15993-8. doi: 10.1073/pnas.1414063111. Epub 2014 Oct 29.

24.

Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease.

Cai Y, Myint W, Paulsen JL, Schiffer CA, Ishima R, Kurt Yilmaz N.

J Chem Theory Comput. 2014 Aug 12;10(8):3438-3448. Epub 2014 Jun 12.

25.

Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease.

Ragland DA, Nalivaika EA, Nalam MN, Prachanronarong KL, Cao H, Bandaranayake RM, Cai Y, Kurt-Yilmaz N, Schiffer CA.

J Am Chem Soc. 2014 Aug 27;136(34):11956-63. doi: 10.1021/ja504096m. Epub 2014 Aug 18.

26.

Burial of nonpolar surface area and thermodynamic stabilization of globins as a function of chain elongation.

Jennaro TS, Beaty MR, Kurt-Yilmaz N, Luskin BL, Cavagnero S.

Proteins. 2014 Oct;82(10):2318-31. doi: 10.1002/prot.24590. Epub 2014 May 12.

PMID:
24752983
27.

HIV-1 protease-substrate coevolution in nelfinavir resistance.

Kolli M, Ozen A, Kurt-Yilmaz N, Schiffer CA.

J Virol. 2014 Jul;88(13):7145-54. doi: 10.1128/JVI.00266-14. Epub 2014 Apr 9.

28.

Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics.

Knight AM, Culviner PH, Kurt-Yilmaz N, Zou T, Ozkan SB, Cavagnero S.

ACS Chem Biol. 2013;8(6):1195-204. doi: 10.1021/cb400030n. Epub 2013 Apr 5.

PMID:
23517476
29.

Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease.

Foulkes-Murzycki JE, Rosi C, Kurt Yilmaz N, Shafer RW, Schiffer CA.

ACS Chem Biol. 2013 Mar 15;8(3):513-8. doi: 10.1021/cb3006193. Epub 2012 Dec 27.

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