Welcome to the SCSB Macromolecular X-ray Laboratory |
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PUBLICATIONS | Last Update: Jun 20, 2024. |
| These are Structural publications from the Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory faculty and staff. | |
2024 ∨ ∧ ⊗ |
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Protein SUMOylation promotes cAMP-independent EPAC1 activation.
1: Yang W, Mei FC, Lin W, White MA, Li L, Li Y, Pan S, Cheng X. Cell Mol Life Sci.2024 Jul 4;81(1):283. doi: 10.1007/s00018-024-05315-y. PMID: 38963422. {PM} {PDF} |
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A new family of bacterial ribosome hibernation factors.
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV. Nature. 2024 Feb;626(8001):1125-1132. doi: 10.1038/s41586-024-07041-8. Epub 2024 Feb 14. {PM} {} |
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Mechanistic insights into the alternative ribosome recycling by HflXr.
Seely SM, Basu RS, Gagnon MG. Nucleic Acids Res. 2024 Apr 24;52(7):4053-4066. doi: 10.1093/nar/gkae128. Erratum in: Nucleic Acids Res. 2024 Apr 24;52(7):4109. doi: 10.1093/nar/gkae217. {PM} {} |
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The reversible activation of norovirus by metal ions.
Sherman M, Cox F, Smith H, Habib MH, Karst S, Wobus CE, Smith TJ. J Virol. 2024 Feb 20;98(2):e0173523. doi: 10.1128/jvi.01735-23. Epub 2024 Jan 18. {PM} {} |
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Protein SUMOylation promotes cAMP-independent EPAC1 activation.
Yang W, Mei FC, Lin W, White MA, Li L, Li Y, Pan S, Cheng X. bioRxiv [Preprint]. 2024 Jan 9:2024.01.08.574738. doi: 10.1101/2024.01.08.574738. {PM} {} |
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Biophysical and structural characterization of a multifunctional viral genome packaging motor.
Prokhorov NS, Davis CR, Maruthi K, Yang Q, Sherman MB, Woodson M, White MA, Miller LM, Jarrold MF, Catalano CE, Morais MC. Nucleic Acids Res. 2024 Jan 25;52(2):831-843. doi: 10.1093/nar/gkad1135. {PM} {} |
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An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano.
Sonani RR, Palmer LK, Esteves NC, Horton AA, Sebastian AL, Kelly RJ, Wang F, Kreutzberger MAB, Russell WK, Leiman PG, Scharf BE, Egelman EH. Nat Commun. 2024 Jan 26;15(1):756. doi: 10.1038/s41467-024-44959-z. {PM} {} |
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High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules.
Tipo J, Gottipati K, Choi KH. RNA. 2024 May 16;30(6):609-623. doi: 10.1261/rna.079796.123. {PM} {} |
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Decoration of Burkholderia Hcp1 protein to virus-like particles as a vaccine delivery platform.
Khakhum N, Baruch-Torres N, Stockton JL, Chapartegui-González I, Badten AJ, Adam A, Wang T, Huerta-Saquero A, Yin YW, Torres AG. Infect Immun. 2024 Mar 12;92(3):e0001924. doi: 10.1128/iai.00019-24. Epub 2024 Feb 14. {PM} {} |
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Structural and functional characterization of the IgSF21-neurexin2α complex and its related signaling pathways in the regulation of inhibitory synapse organization.
Chofflet N, Naito Y, Pastore AJ, Padmanabhan N, Nguyen PT, Poitras C, Feller B, Yi N, Van Prooijen J, Khaled H, Coulombe B, Clapcote SJ, Bourgault S, Siddiqui TJ, Rudenko G, Takahashi H. Front Mol Neurosci. 2024 Mar 20;17:1371145. doi: 10.3389/fnmol.2024.1371145. {PM} {} |
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Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance.
Rybak MY, Gagnon MG. Nat Struct Mol Biol. 2024 May;31(5):810-816. doi: 10.1038/s41594-024-01236-3. Epub 2024 Mar 27. {PM} {} |
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Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site.
Tipo J, Gottipati K, Slaton M, Gonzalez-Gutierrez G, Choi KH. Nat Commun. 2024 May 17;15(1):4198. doi: 10.1038/s41467-024-48162-y. {PM} {} |
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An interaction network in the polymerase active site is a prerequisite for Watson-Crick basepairing in Pol γ.
Park J, Herrmann GK, Roy A, Shumate CK, Cisneros GA, Yin YW. Sci Adv. 2024 May 24;10(21):eadl3214. doi: 10.1126/sciadv.adl3214. Epub 2024 May 24. {PM} {} |
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2023 ∨ ∧ ⊗ |
PubMed 2023 |
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Structural and Molecular Basis for Mitochondrial DNA Replication and Transcription in Health and Antiviral Drug Toxicity.
Park J, Baruch-Torres N, Yin YW. Molecules. 2023 Feb 14;28(4):1796. doi: 10.3390/molecules28041796. {PM} {} |
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D'Ann Rochon(1955-2022), a life of passion for plant virology.
Sanfaçon H, Alam SB, Ghoshal B, Ghoshal K, Hui E, Jackson AO, Kakani K, Morris TJ, Nagy PD, Simon AE, Sit TL, Smith TJ, White KA, Xiang Y. Virology. 2023 Oct;587:109874. doi: 10.1016/j.virol.2023.109874. Epub 2023 Sep 8. {PM} {} |
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Polymerase 1 in Nuclear and Mitochondrial Base Excision Repair.
Herrmann GK, Yin YW. The Role of Poly(ADP-ribose) Biomolecules. 2023 Jul 31;13(8):1195. doi:10.3390/biom13081195. {PM} {} |
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Insights into themolecular mechanism's of translation inhibition by the ribosome-targeting antibiotic thermorubin.
Paranjpe MN, Marina VI, Grachev AA, Maviza TP, Tolicheva OA, Paleskava A,Osterman IA, Sergiev PV, Konevega AL, Polikanov YS, Gagnon MG. Nucleic Acids Res. 2023 Jan 11;51(1):449-462. doi:10.1093/nar/gkac1189. {PM} {} |
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Structural basis for cloverleaf RNA-initiated viral genome replication.
Gottipati K, McNeme SC, Tipo J, White MA, Choi KH. Nucleic Acids Res. 2023 Sep 8;51(16):8850-8863. doi: 10.1093/nar/gkad618. {PM} {} |
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Polγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.
Park J, Herrmann GK, Mitchell PG, Sherman MB, Yin YW. Nat Struct Mol Biol. 2023 Jun;30(6):812-823. doi: 10.1038/s41594-023-00980-2. Epub 2023 May 18. {PM} {} |
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Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.
Seely SM, Parajuli NP, De Tarafder A, Ge X, Sanyal S, Gagnon MG. Nat Commun. 2023 Aug 3;14(1):4666. doi: 10.1038/s41467-023-40416-5. {PM} {} |
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Neck and capsid architecture of the robust Agrobacterium phage Milano.
Sonani RR, Esteves NC, Horton AA, Kelly RJ, Sebastian AL, Wang F, Kreutzberger MAB, Leiman PG, Scharf BE, Egelman EH. Commun Biol. 2023 Sep 8;6(1):921. doi:10.1038/s42003-023-05292-1. {PM} {} |
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Designer molecules of the synaptic organizer MDGA1 reveal 3D conformational control of biological function.
Lee H, Chofflet N, Liu J, Fan S, Lu Z, Resua Rojas M, Penndorf P, Bailey AO,Russell WK, Machius M, Ren G, Takahashi H, Rudenko G. J Biol Chem. 2023 Apr;299(4):104586. doi: 10.1016/j.jbc.2023.104586. Epub 2023 Mar 7. {PM} {} |
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A highly selective humanized DDR1 mAb reverses immune exclusion by disrupting collagen fiber alignment in breast cancer.
Liu J, Chiang HC, Xiong W, Laurent V, Griffiths SC, Dülfer J, Deng H, Sun X,Yin YW, Li W, Audoly LP, An Z, Schürpf T, Li R, Zhang N. J Immunother Cancer. 2023 Jun;11(6):e006720. doi:10.1136/jitc-2023-006720. {PM} {} |
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Maintenance of Flap Endonucleases for Long-Patch Base Excision DNA Repair in Mouse Muscle and Neuronal Cells Differentiated In Vitro.
Caston RA, Fortini P, Chen K, Bauer J, Dogliotti E, Yin YW, Demple B. Int J Mol Sci. 2023 Aug 12;24(16):12715. doi: 10.3390/ijms241612715. {PM} {} |
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Biophysical and structural characterization of a multifunctional viral genome packaging motor.
Prokhorov NS, Davis CR, Maruthi K, Yang Q, Sherman MB, Woodson M, White MA, Miller LM, Jarrold MF, Catalano CE, Morais MC. Nucleic Acids Res. 2023 Dec 12:gkad1135. doi: 10.1093/nar/gkad1135. Epub ahead of print. {PM} {PDF} |
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Binding of microRNA-122 to the hepatitis C virus 5' untranslated region modifies interactions with poly(C) binding protein 2 and the NS5B viral polymerase.
Scott S, Li Y, Bermek O, Griffith JD, Lemon SM, Choi KH. Nucleic Acids Res. 2023 Dec 11;51(22):12397-12413. doi: 10.1093/nar/gkad1000. {PM} {} |
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2022 ∨ ∧ ⊗ |
PubMed 2022 |
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Environmentally-triggered contraction of the norovirus virion determines diarrheagenic potential.
Helm EW, Peiper AM, Phillips M, Williams CG, Sherman MB, Kelley T, Smith HQ, Jacobs SO, Shah D, Tatum SM, Iyer N, Grodzki M, Morales Aparicio JC, Kennedy EA, Manzi MS, Baldridge MT, Smith TJ, Karst SM. Front. Immunol. 2022 Nov 1;13:1043746. doi: 10.3389/fimmu.2022.1043746. {PM} {} |
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Chemically targeting the redox switch in AP1 transcription factor ΔFOSB.
Kumar A, Aglyamova G, Yim YY, Bailey AO, Lynch HM, Powell RT, Nguyen ND, Rosenthal Z, Zhao WN, Li Y, Chen J, Fan S, Lee H, Russell WK, Stephan C, Robison AJ, Haggarty SJ, Nestler EJ, Zhou J, Machius M, Rudenko G. Nucleic Acids Research. 2022 Sep 9;50(16):9548-9567, https://doi.org/10.1093/nar/gkab710 {PM} {PDF} |
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Editorial: Nucleic Acid Polymerases: The Two-Metal-Ion Mechanism and Beyond.
Pata JD, Yin YW, Lahiri I. Front Mol Biosci. 2022 Jul 13;9:948326. doi:10.3389/fmolb.2022.948326. {PM} {} |
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Characterization of a Primordial Major Capsid-Scaffolding Protein Complex in Icosahedral Virus Shell Assembly.
Davis CR, Backos D, Morais MC, Churchill MEA, Catalano CE. J Mol Biol. 2022 Oct 15;434(19):167719. doi:10.1016/j.jmb.2022.167719. Epub 2022 Jul 9. {PM} {} |
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Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase.
Fraser A, Sokolova ML, Drobysheva AV, Gordeeva JV, Borukhov S, Jumper J, Severinov KV, Leiman PG. Nat Commun. 2022 Jun 20;13(1):3526. doi: 10.1038/s41467-022-31214-6. {PM} {PDF} |
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Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation.
Basu RS, Sherman MB, Gagnon MG. Nat Commun. 2022 Jun 13;13(1):3388. doi: 10.1038/s41467-022-31129-2. {PM} {} |
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Distinct dissociation rates of murine and human norovirus P-domain dimers suggest a role of dimer stability in virus-host interactions.
Creutznacher R, Maass T, Dülfer J, Feldmann C, Hartmann V, Lane MS, Knickmann J, Westermann LT, Thiede L, Smith TJ, Uetrecht C, Mallagaray A, Waudby CA, Taube S, Peters T. Commun Biol. 2022 Jun 9;5(1):563. doi: 10.1038/s42003-022-03497-4. {PM} {} |
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Mechanisms of ribosome recycling in bacteria and mitochondria: a structural perspective.
Seely SM, Gagnon MG. RNA Biol. 2022;19(1):662-677. doi:10.1080/15476286.2022.2067712. Epub 2021 Dec 31. {PM} {} |
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Epac1 activation by cAMP regulates cellular SUMOylation and promotes the formation of biomolecular condensates.
Yang W, Robichaux WG 3rd, Mei FC, Lin W, Li L, Pan S, White MA, Chen Y, Cheng X. Sci Adv. 2022 Apr 22;8(16):eabm2960. doi: 10.1126/sciadv.abm2960. Epub 2022 Apr 20. {PM} {PDF} |
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Human Mitochondrial DNA Polymerase Metal Dependent UV Lesion Bypassing Ability.
Park J, Baruch-Torres N, Iwai S, Herrmann GK, Brieba LG, Yin YW. Front Mol Biosci. 2022 Mar 9;9:808036. doi: 10.3389/fmolb.2022.808036. {PM} {} |
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2021 ∨ ∧ ⊗ |
PubMed 2021 |
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Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor
Joshua Pajak, Erik Dill, Emilio Reyes-Aldrete, Mark A White, Brian A Kelch, Paul J Jardine, Gaurav Arya, Marc C Morais. Nucleic Acids Research. 2021 gkab372, May 29, https://doi.org/10.1093/nar/gkab372 {PM} {PDF} |
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Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase.
Lee E, Bujalowski PJ, Teramoto T, Gottipati K, Scott SD, Padmanabhan R, Choi KH. Nat Commun. 2021 May 5;12(1):2530. doi: 10.1038/s41467-021-22846-1. {PM} {PDF} |
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A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA.
Woodson M, Pajak J, Mahler BP, Zhao W, Zhang W, Arya G, White MA, Jardine PJ, Morais MC. Sci Adv. 2021 May 7;7(19), eabc1955. doi: 10.1126/sciadv.abc1955. {PM} {PDF} |
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Interplay between hevin, SPARC, and MDGAs: modulators of neurexin-neuroligin transsynaptic bridges.
Fan S, Gangwar SP, Machius M, Rudenko G. Structure. 2021 Jan 29:S0969-2126(19)00003-4. doi: 10.1016/j.str.2021.01.003. Online ahead of print. {PM} {PDF} |
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Structure and function of virion RNA polymerase of a crAss-like phage.
Drobysheva AV, Panafidina SA, Kolesnik MV, Klimuk EI, Minakhin L, Yakunina MV, Borukhov S, Nilsson E, Holmfeldt K, Yutin N, Makarova KS, Koonin EV, Severinov KV, Leiman PG, Sokolova ML. Nature. 2021 Jan :589(7841):306-309. doi: 10.1038/s41586-020-2921-5. Epub 2020 Nov 18. {PM} {PDF} |
2020 ∨ ∧ ⊗ |
PubMed 2020 |
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Structural basis for ribosome recycling by RRF and tRNA.
Zhou D, Tanzawa T, Lin J, Gagnon MG. Nat Struct Mol Biol. 2020 27(1):25-32. doi: 10.1038/s41594-019-0350-7. {PM} {PDF} |
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Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28.
Reyes-Aldrete E, Dill EA, Bussetta C, Szymanski MR, Diemer G, Maindola P, White MA, Bujalowski WM, Choi KH, Morais MC. Viruses. 2020 Dec 23;13(1):15. doi: 10.3390/v13010015. {PM} {PDF} |
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Structure and Function of the T4 Spackle Protein Gp61.3.
Kanamaru S, Uchida K, Nemoto M, Fraser A, Arisaka F, Leiman PG. Viruses. 2020 Sep 24;12(10):1070. doi: 10.3390/v12101070. {PM} {PDF} |
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Discovery of COVID-19 Inhibitors Targeting the SARS-CoV-2 Nsp13 Helicase.
White MA, Lin W, Cheng X. J Phys Chem Lett. 2020 Oct 14:9144-9151. doi: 10.1021/acs.jpclett.0c02421. Online ahead of print. {PM} {PDF} |
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Highly Conserved Molecular Features in IgLONs Contrast Their Distinct Structural and Biological Outcomes.
Venkannagari H, Kasper JM, Misra A, Rush SA, Fan S, Lee H, Sun H, Seshadrinathan S, Machius M, Hommel JD, Rudenko G. J. Mol. Biol. 2020,Sep 4: 432(19):5287-5303. doi: 10.1016/j.jmb.2020.07.014. Epub 2020 Jul 22. {PM} {PDF} |
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Discovery of phenanthridine analogues as novel chemical probes disrupting the binding of DNA to ΔFosB homodimers and ΔFosB/JunD heterodimers. Yi Li, Zhiqing Liu, Galina Aglyamova, Jianping Chen, Haiying Chen, Mukund Bhandari, Mark A.White, Gabrielle Rudenko, JiaZhou. Bioorganic & Medicinal Chemistry Letters Volume 30, Issue 16, 15 August 2020, 127300; https://doi.org/10.1016/j.bmcl.2020.127300 {PM} {PDF} |
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Mutational Analysis of the Structure and Function of the Chaperoning Domain of UNC-45B.
Gaziova I, Moncrief T, Christian CJ, Villarreal M, Powell S, Lee H, Qadota H, White MA, Benian GM, Oberhauser AF. Biophysics J. 2020, Jul 22: S0006-3495(20)30562-2. doi: 10.1016/j.bpj.2020.07.012. Online ahead of print. {PM} {PDF} |
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A cocrystal structure of dengue capsid protein in complex of inhibitor.
Hongjie Xia, Xuping Xie, Jing Zou, Christian G Noble, William K Russell, Luis Marcelo F Holthauzen, Kyung H Choi, Mark A White, Pei-Yong Shi. PNAS USA 2020, July 15 first published July 15, 2020; https://doi.org/10.1073/pnas.2003056117 {PM} {PDF} |
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Self-Assembly of Block Heterochiral Peptides into Helical Tapes.
Clover TM, O'Neill CL, Appavu R, Lokhande G, Gaharwar AK, Posey AE, White MA, Rudra JS. J Am Chem Soc. 2020 May 1. doi: 10.1021/jacs.9b09755. Online ahead of print. {PM} {PDF} |
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The Interplay between Molten Globules and Heme Disassociation Defines Human Hemoglobin Disassembly.
Premila P.Samuel, Mark A.White, William C.Ou, David A.Case, George N.Phillips Jr., John S.Olson. Biophysical Journal 2020 Feb 4; https://doi.org/10.1016/j.bpj.2020.01.031 {PM} {PDF} |
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Structural Energy Landscapes and Plasticity of the Microstates of Apo E. coli cAMP Receptor Protein. Chkheidze R, Evangelista W, White MA, Yin YW, Lee JC. Biochemistry 2020 Feb 4;59(4):460-470. doi: 10.1021/acs.biochem.9b00895. Epub 2020 Jan 10. {PM} {PDF} |
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Self-assembly of the bZIP transcription factor ΔFosB.
Zhou Yin, Harikanth Venkannagari, Haley Lynch,Galina Aglyamova, Mukund Bhandari, Mischa Machius, Eric J. Nestler, Alfred J.Robison, Gabby Rudenko. Current Research in Structural Biology Volume 2, 2020; pg. 1-13 https://doi.org/10.1016/j.crstbi.2019.12.001. {PM} {PDF} |
2019 ∨ ∧ ⊗ |
PubMed 2019 |
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Conformational States of Exchange Protein Directly Activated by cAMP (EPAC1) Revealed by Ensemble Modeling and Integrative Structural Biology.
White MA, Tsalkova T, Mei FC, Cheng X. Cells 2020, 9(1), 35. doi: 10.3390/cells9010035. On-line 2019 Dec 21. {PM} {PDF} |
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Differential modulation of energy landscapes of cyclic AMP receptor protein (CRP) as a regulatory mechanism for class II CRP-dependent promoters.
Wilfredo Evangelista, Aichun Dong, Mark A White, Jianquan Li, J Ching Lee J Biol Chem. 2019 Oct 18;294(42):15544-15556. doi: 10.1074/jbc.RA119.009151. Epub 2019 Sep 6. {PM} {PDF} |
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Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120.
Michel Plattner, Mikhail M.Shneider, Nikolay P.Arbatsky, Alexander S.Shashkov, Alexander O.Chizhov, SergeyNazarov, Nikolai S.Prokhorov, Nicholas M.I.Taylor, Sergey A.Buth, MichelaGambino, Yilmaz EmreGencay, LoneBrøndsted, Elizabeth M.Kutter, Yuriy A.Knirel, Petr G.Leiman. J. Mol. Biol. 2019 , July 22, EPub {PM} {PDF} |
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Networked Communication between Polymerase and Exonuclease Active Sites in Human Mitochondrial DNA Polymerase.
Sowers ML, Anderson APP, Wrabl JO, Yin YW. J Am Chem Soc.. 2019 Jul 10; 141(27): {PM} {PDF} |
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Editorial overview: Synapses: bridging the gap between their structure and function.
Rudenko G, Takahashi H. Curr Opin Struct Biol.. 2019 Feb; 54:iii-vii {PM} {PDF} |
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The Dynamic Capsid Structures of the Noroviruses.
Hong Q Smith, Thomas J Smith. Viruses 2019 11(3), March, 235 {PM} {PDF} |
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Glutamate Dehydrogenase, a Complex Enzyme at a Crucial Metabolic Branch Point.
Smith HQ, Li C, Stanley CA, Smith TJ. Neurochem Res. 2019 Jan; 44(1):117-132 {PM} {PDF} |
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Glutamate dehydrogenase: Structure of a hyperinsulinism mutant, corrections to the atomic model, and insights into a regulatory site.
Nassar OM, Li C, Stanley CA, Pettitt BM, Smith TJ. Proteins. 2019 Jan;87(1):41-50. doi: 10.1002/prot.25620. Epub 2018 Nov 18. {PM} {PDF} |
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Design, Synthesis, and Characterization of 4-Undecylpiperidine-2-carboxamides as Positive Allosteric Modulators of the Serotonin (5-HT) 5-HT2C Receptor.
Wild CT, Miszkiel JM, Wold EA, Soto CA, Ding C, Hartley RM, White MA, Anastasio NC, Cunningham KA, Zhou J. J Med Chem. 2019 Jan 10;62(1):288-305 {PM} {PDF} |
2018 ∨ ∧ ⊗ |
PubMed 2018 |
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Structural Plasticity of Neurexin 1α: Implications for its Role as Synaptic Organizer.
Jianfang Liu†, Anurag Misra†, Sekhar Reddy, Mark Andrew White, Gang Ren, Gabby Rudenko. JMB. 2018 Sept. 5; doi: 10.1016/j.jmb.2018.08.026. {PM} {PDF} |
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FerA is a Membrane-Associating Four-Helix Bundle Domain in the Ferlin Family of Membrane-Fusion Proteins.
Harsini FM, Chebrolu S, Fuson KL, White MA, Rice AM, Sutton RB. Sci Rep. 2018Jul 19;8(1):10949. doi: 10.1038/s41598-018-29184-1. {PM} {PDF} |
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Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design.
Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Annu Rev Biochem. 2018 Jun 20;87:451-478. doi: 10.1146/annurev-biochem-062917-011942. Epub 2018 Mar 23. {PM} {PDF} |
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Contractile injection systems of bacteriophages and related systems.
Taylor NMI, van Raaij MJ, Leiman PG. Mol Microbiol. 2018 Apr;108(1):6-15. doi: 10.1111/mmi.13921. Epub 2018 Feb 26. {PM} {PDF} |
2017 ∨ ∧ ⊗ |
PubMed 2017 |
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Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges.
Gangwar SP, Zhong X, Seshadrinathan S, Chen H, Machius M, Rudenko G. Neuron. 2017 Jun 21;94(6):1132-1141.e4. doi: 10.1016/j.neuron.2017.06.009. {PM} {PDF} |
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A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease.
Szymanski MR, Yu W, Gmyrek AM, White MA, Molineux IJ, Lee JC, Yin YW. Nat Commun. 2017 May 3;8:14959. doi: 10.1038/ncomms14959. {PM} {PDF} |
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Interactions between the Dengue Virus Polymerase NS5 and Stem-Loop A.
Bujalowski PJ, Bujalowski W, Choi KH. J Virol. 2017 May 12;91(11). pii: e00047-17. doi: 10.1128/JVI.00047-17. Print 2017 Jun 1. {PM} {PDF} |
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Dynamic Control of Synaptic Adhesion and Organizing Molecules in Synaptic Plasticity.
Rudenko G. Neural Plast. 2017;2017:6526151. doi: 10.1155/2017/6526151. Epub 2017 Jan 31. Review. {PM} {PDF} |
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Reversible stacking of lipid nanodiscs for structural studies of clotting factors.
Kirill Grushin, Mark Andrew White, and Svetla Stoilova-McPhie. Nanotechnology Reviews 2017;6(1): 139-148. doi: 10.1515/ntrev-2016-0073 {PM} {PDF} |
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Functional analysis of rare variants found in schizophrenia implicates a critical role for GIT1-PAK3 signaling in neuroplasticity.
Kim MJ, Biag J, Fass DM, Lewis MC, Zhang Q, Fleishman M, Gangwar SP, Machius M, Fromer M, Purcell SM, McCarroll SA, Rudenko G, Premont RT, Scolnick EM, Haggarty SJ. Mol Psychiatry.2017 Mar;22(3):417-429. doi: 10.1038/mp.2016.98. Epub 2016 Jul 26. {PM} {PDF} |
2016 ∨ ∧ ⊗ |
PubMed 2016 |
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Structural and mechanistic insights into regulation of the retromer coat by TBC1d5.
Jia D, Zhang JS, Li F, Wang J, Deng Z, White MA, Osborne DG, Phillips-Krawczak C, Gomez TS, Li H, Singla A, Burstein E, Billadeau DD, Rosen MK. Nat Commun.. 2016 Nov 9;7:13305. doi: 10.1038/ncomms13305 {PM} {PDF} |
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Molecular Architecture of Contactin-associated Protein-like 2 (CNTNAP2) and its Interaction with Contactin 2 (CNTN2),
Lu Z, Reddy MV, Liu J, Kalichava A, Liu J, Zhang L, Chen F, Wang Y, Holthauzen LM, White MA, Seshadrinathan S, Zhong X, Ren G, Rudenko G., J Biol Chem. 2016 Sep 12. pii: jbc.M116.748236. {PM} {PDF} |
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DNA Polymerase-? R953C Mutant is Associated with ART-Induced Mitochondrial Toxicity.,
Li M, Mislak AC, Foli Y, Agbosu E, Bose V, Bhandari S, Szymanski MR, Shumate CK, Yin YW, Anderson KS, Paintsil E., Antimicrob Agents Chemother. 2016 Jul 5. pii: AAC.00976-16. {PM} {PDF} |
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Pestivirus Npro directly interacts with interferon regulatory factor 3 (IRF3) monomer and dimer.,
Gottipati K, Holthauzen LM, Ruggli N, Choi KH., J Virol. 2016 Jun 22. pii: JVI.00318-16. {PM} {PDF} |
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The yeast mitochondrial RNA polymerase and transcription factor complex catalyzes efficient priming of DNA synthesis on single-stranded DNA.,
Ramachandran A, Nandakumar D, Deshpande A, Lucas TP, Bhojappa RR, Tang GQ, Raney K, Yin YW, Patel SS., J Biol Chem. 2016 Jun 16. pii: jbc.M116.740282. {PM} {PDF} |
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Stereospecific effects of oxygen-to-sulfur substitution in DNA phosphate on ion-pair dynamics and protein-DNA affinity.,
Nguyen D, Zandarashvili L, White MA, Iwahara J., Chembiochem. 2016 Jun 7. doi: 10.1002/cbic.201600265. {PM} {PDF} |
 |
Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor.,
Mao H, Saha M, Reyes-Aldrete E, Sherman MB, Woodson M, Atz R, Grimes S, Jardine PJ, Morais MC., Cell Rep. 2016 Mar 1;14(8):2017-29. doi: 10.1016/j.celrep.2016.01.058. {PM} {PDF} |
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Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface.,
Klema VJ, Ye M, Hindupur A, Teramoto T, Gottipati K, Padmanabhan R, Choi KH., PLoS Pathog. 2016 Feb 19;12(2):e1005451. {PM} {PDF} |
2015 ∨ ∧ ⊗ |
PubMed 2015 |
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Yeast Mitochondrial Transcription Factor Mtf1 Determines the Precision of Promoter-Directed Initiation of RNA Polymerase Rpo41.,
Yang X, Chang HR, Yin YW., PLoS One. 2015 Sep 2;10(9):e0136879. {PM} {PDF} |
 |
Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.
Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J., Biophys J. 2015 Sep 1;109(5):1026-37. {PM} {PDF} |
 |
Flaviviral Replication Complex: Coordination between RNA Synthesis and 51-RNA Capping.,
Klema VJ, Padmanabhan R, Choi KH. Viruses. 2015 Aug 13;7(8):4640-56. {PM} {PDF} |
 |
Transcription yield of fully 2'-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants,
Meyer AJ, Garry DJ, Hall B, Byrom MM, McDonald HG, Yang X, Yin YW, Ellington AD., Nucleic Acids Res. 2015 Jul 24. {PM} {PDF} |
 |
Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase?
Sohl CD, Szymanski MR, Mislak AC, Shumate CK, Amiralaei S, Schinazi RF, Anderson KS, Yin YW., Proc Natl Acad Sci U S A. 2015 June 29, 201421733 {PM} {PDF} |
 |
Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase
Szymanski MR, Kuznetsov VB, Shumate C, Meng Q, Lee YS, Patel G, Patel S, Yin YW., EMBO J. 2015 June 8, e201591520 {PM} {PDF} |
 |
Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1
Zandarashvili L, White MA, Esadze A, Iwahara J, FEBS Lett. 2015 May 19, S0014-5793(15) 00398-1. {PM} {PDF} |
2014 ∨ ∧ ⊗ |
PubMed 2014 |
 |
Small-molecule Bax agonists for cancer therapy
Meiguo Xin, Rui Li, Maohua Xie, Dongkyoo Park, Taofeek K. Owonikoko, Gabriel L. Sica, Patrick E. Corsino, Jia Zhou, Chunyong Ding, Mark A. White, Andrew T. Magis, Suresh S. Ramalingam, Walter J. Curran, Fadlo R. Khuri & Xingming Deng, Nature Communications 5, 2014. Epub Sept 17. {PM} {PDF} |
 |
ent-Kaurane-Based Regio- and Stereoselective Inverse Electron Demand Hetero-Diels-Alder Reactions: Synthesis of Dihydropyran-Fused Diterpenoids
Chunyong Ding, Lili Wang, Haijun Chen, Christopher Wild, Na Ye, Ye Ding, Tianzhi Wang, Mark A White, Qiang Shen, and Jia Zhou, Org. Biomol. Chem., 2014. Epub Sept 3. {PM} {PDF} |
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Ch. 11. Mitochondrial DNA and RNA Polymerases, (Ed. Katsuhiko S. Murakami & Michael A. Trakselis)
Y. Whitney Yin, Nucleic Acids and Polymerases 2014;11:251-276. {PM} {PDF} |
 |
Use of Small-Angle X-ray Scattering to Investigate the Structure and Function of Dengue Virus NS3 and NS5.
Choi KH. and Morais MC, Dengue, Methods Mol Biol 2014;1138:241-52. {PM} {PDF} |
2013 ∨ ∧ ⊗ |
PubMed 2013 |
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The structure of classical swine fever virus N(pro): a novel cysteine Autoprotease and zinc-binding protein involved in subversion of type I interferon induction.,
Gottipati K, Ruggli N, Gerber M, Tratschin JD, Benning M, Bellamy H, Choi KH., PLoS Pathog. 2013;9(10):e1003704. Epub 2013 Oct 17. {PM} {PDF} |
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Oridonin Ring A-Based Diverse Constructions of Enone Functionality: Identification of Novel Dienone Analogues Effective for Highly Aggressive Breast Cancer by Inducing Apoptosis,
Ding C, Zhang Y, Chen H, Yang Z, Wild C, Ye N, Ester CD, Xiong A, White MA, Shen Q, Zhou J., J Med Chem. 2013 Oct 31. Epub: Oct 31 {PM} {PDF} |
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Design of Metastable Β-Sheet Oligomers from Natively Unstructured Peptide,
Guerrero-Muñoz MJ, Castillo-Carranza DL, Sengupta U, White MA, Kayed R, ACS Chem Neurosci 2013 Dec 184 4(12):1520-3 Epub: Oct 14 {PM} {PDF} |
 |
Intrinsic flexibility of West Nile virus protease in solution characterized using small-angle X-ray scattering,
Garces AP, Watowich SJ., Biochemistry 2013 Oct 1 52(39):6856-65 Epub: Sept 20 {PM} {PDF} |
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Exonuclease Of Human Dna Polymerase Gamma Disengages Its Strand Displacement Function,
Quan He,Christie K. Shumate, Mark A White, Ian J. Molineux, Y. Whitney Yin, Mitochondrion 2013 Aug 30 13(6) 592-601. Epub: Aug 29 {PM} {PDF} |
 |
Preparation, characterization, and transport of dexamethasone-loaded polymeric nanoparticles across a human placental in vitro model,
Hazem Ali, Irina Kalashnikova, Mark Andrew White, Michael Sherman, and Erik Rytting, Int. J. Pharmaceuticals 2013 454(1) 149-57. Epub: July 12 {PM} {PDF} |
 |
Overcoming Synthetic Challenges of Oridonin A-Ring Structural Diversification: Regio- and Stereoselective Installation of Azides and 1,2,3-Triazoles at the C-1, C-2, or C-3 Position,
Chunyong Ding, Yusong Zhang, Haijun Chen, Christopher Wild, Tianzhi Wang, Mark A. White, Qiang Shen, Jia Zhou, Organic Letters 2013 Jul 19 15(14) 3718-21. Epub: July 8 {PM} {PDF} |
 |
Efficient Synthesis of ESI-09, A Novel Non-cyclic Nucleotide EPAC Antagonist,
Haijun Chen, Chunyong Ding, Christopher Wild, Huiling Liu, Tianzhi Wang, Mark A. White, Xiaodong Cheng, Jia Zhou, Tetrahedron Lett. 2013 54 1546-1549. Epub: Jan. 21 {PM} {PDF} |
2012 ∨ ∧ ⊗ |
PubMed 2012 |
 |
Structural analyses of a constitutively active mutant of exchange protein directly activated by cAMP.,
White MA, Li S, Tsalkova T, Mei FC, Liu T, Woods VL Jr, Cheng X., PLoS One. 2012;7(11):e49932. Epub: 2012 Nov 26. {PM} {PDF} |
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Dengue virus nonstructural protein 5 adopts multiple conformations in solution.
Bussetta C, Choi KH., Biochemistry. 2012 Jul 31;51 (30):5921-31 Epub: Jul 16 {PM} {PDF} |
 |
Dual catalysis mode for the dicarbonyl reduction catalyzed by diketoreductase
Meiling Lu, Yan Huang, Mark A. White, Xuri Wu, Nan Liu, Xiaodong Cheng and Yijun Chen, Chem. Commun. 2012;48: 11352-11354 {PM} {PDF} |
 |
Divergence of multimodular polyketide synthases revealed by a didomain structure.
Zheng J, Gay DC, Demeler B, White MA, Keatinge-Clay AT., Nat Chem Biol 2012 964 Epub: May 27 {PM} {PDF} |
 |
The dsDNA packaging motor in bacteriophage φ29.,
Morais MC., Adv Exp Med Biol. 2012;726:511-47. Review. {PM} {PDF} |
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Viral polymerases.,
Choi KH., Adv Exp Med Biol. 2012;726:267-304. Review. {PM} {PDF} |
2011 ∨ ∧ ⊗ | PubMed 2011 |
 |
Mechanism of Intracellular cAMP Sensor Epac2 Activation: cAMP-induced conformational changes identified by peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS).
Sheng Li, Tamara Tsalkova, Mark A. White, Fang C. Mei, Tong Liu, Daphne Wang, Virgil L. Woods Jr. and Xiaodong Cheng J Biol Chem. 2011 286(20);17889-97 Epub: March 17 {PM} {Review} {PDF} |
2010 ∨ ∧ ⊗ | PubMed 2010 |
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Structural basis for substrate specificity of alphavirus nsP2 proteases.
Russo AT, Malmstrom RD, White MA, Watowich SJ. J Mol Graph Model. 2010; 29(1);46-53 Epub]: Apr 24 {PM} {PDF} |
2009 ∨ ∧ ⊗ | PubMed 2009 |
 |
Mechanism of EPAC activation: Structural and functional analyses of EPAC2 hinge mutants with constitutive and reduced activities.
Tsalkova T, Blumenthal DK, Mei FC, White MA, Cheng X. J Biol Chem. 2009; 284(35);23644-51 Epub: Jun 24 {PM} {PDF} |
 |
The c2 domains of human synaptotagmin 1 have distinct mechanical properties,
Fuson KL, Ma L, Sutton RB, Oberhauser AF, Biophys J. 2009; 963);1083-90 EPUB: {PM} {PDF} |
2008 ∨ ∧ ⊗ | PubMed 2008 |
 |
The Use of Complementary Cation and Anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1,
Mark Andrew White, Natalia Mast, Ingemar Bjorkhem, Eric F. Johnson, C. David Stout, and Irina A. Pikuleva, Acta Cryst. D 2008; 65(16);487-95 EPUB: April 20. {PM} {PDF} |
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Crystal structures of substrate-bound and substrate-free cytochrome P450 46A1, the principle cholesterol hydroxylase in the brain,
Natalia Mast, Mark Andrew White, Ingemar Bjorkhem, Eric F. Johnson, C. David Stout, and Irina A. Pikuleva, PNAS 2008; 105(28);9546-9551 EPUB: July 9. {PM} {PDF} |
2007 ∨ ∧ ⊗ | PubMed 2007 |
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Structure of Human Synaptotagmin 1 C2A-C2B in the Absence of Ca2+ Reveals a Novel Domain Association,
Fuson, K.L., Montes, M., Robert, J. J., Sutton R. B., Biochemistry 2008; 46(45);13041-13048 EPUB: Oct. 23. {PM} {PDF} |
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Structural and Thermodynamic Consequences of 1-(4-Chlorophenyl)imidazole Binding to Cytochrome P450 2B4.
Zhao Y, Sun L, Muralidhara BK, Kumar S, White MA, Stout CD, Halpert JR., Biochemistry 2007 Oct 16;46(41):11559-67. EPUB: Sept 22. {PM} {PDF} |
2006 ∨ ∧ ⊗ | PubMed 2006 |
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The crystal structure of the E. coli stress protein YciF.
Aditya Hindupur, Deqian Liu, Yonghong Zhao, Henry D. Bellamy, Mark A. White, and Robert O. Fox, Protein Science 2006 EPUB: Sept 25. {PM} {PDF} |
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The Crystal Structure of the Venezuelan Equine Encephalitis Alphavirus nsP2 Protease.
Andrew T. Russo, Mark A. White, and Stanley J. Watowich, Structure 2006 14: 1449-1458. {PM} {PDF} |
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Purification, crystallization and X-ray diffraction analysis of human synaptotagmin 1 C2A-C2B.
Montes M, Fuson KL, Sutton RB, Robert JJ. Acta Cryst. F 62, Page 926-9, Aug 2006. {PM} {PDF} |
 |
Structure of a glutathione conjugate bound to the active site of aldose reductase.
Singh R, White MA, Ramana KV, Petrash JM, Watowich SJ, Bhatnagar A, Srivastava SK., Proteins: Structure, Function, and Bioinformatics 2006, July 1, 64(1), 101-110; [April 25, Epub ahead of print] {PM} {PDF} |
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NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognition.
Mukherjee M, Dutta K, White MA, Cowburn D, Fox RO., Protein Science 2006, June 15(6), 1342-55. {PM} {PDF} |
 |
Russo AT, Watowich SJ,
Purification, crystallization and X-ray diffraction analysis of the C-terminal protease domain of Venezuelan equine encephalitis virus nsP2. Acta Cryst. F 62(6), Page 514-7, June 2006. {PM} {PDF} |
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Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: Insight into P450 conformational plasticity and membrane interaction.
Zhao Y, White MA, Muralidhara BK, Sun L, Halpert JR, Stout CD., J Biol Chem. 2006, March 3, 281(9), 5973-81; [Epub ahead of print: Dec 21] {PM} {PDF} |
 |
Crystal structure of cone arrestin at 2.3A: evolution of receptor specificity.,
Sutton RB, Vishnivetskiy SA, Robert J, Hanson SM, Raman D, Knox BE, Kono M, Navarro J, Gurevich VV., J Mol Biol. 2005 Dec 16;354(5):1069-80. Epub 2005 Nov 2. {PM} {PDF} |
2005 ∨ ∧ ⊗ | PubMed 2005 |
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The crystal structure of the cis-proline to glycine variant (P114G) of ribonuclease A,
Schultz DA, Friedman AM, White MA, Fox RO., Protein Sci. 2005 Nov; 14(11):2862-70. [Epub ahead of print; Sep 30] {PM} {PDF} |
 |
Crystallization and preliminary X-ray diffraction of the ZO-binding domain of human occludin
Bi-Hung Peng, Mark A. White, Gerald A. Campbell, Jebamony J. Robert, J. Ching Lee, Roger B. Sutton, Acta Cryst. F 61, Page 369-371, Apr 2005. {PM} {PDF} |
 |
Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core.
Czerwinski EW, Midoro-Horiuti T, White MA, Brooks EG, Goldblum RM., J. Biol. Chem 280, 5, 3740-6, 2005. {PM} {PDF} |
2004 ∨ ∧ ⊗ | PubMed 2004 |
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Escherichia coli stress protein YciF: expression, crystallization and preliminary crystallographic analysis.
Liu D, Zhao Y, Fan X, Sun Y, Fox RO., Acta Cryst. D 60, Page 2389-90, Dec. 2004. {PM} {PDF} |
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Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9 A resolution: Insight into the range of P450 conformations and coordination of redox partner binding Emily E. Scott, Mark A. White, You Ai He, Eric F. Johnson, C. David Stout, and James R. Halpert, J. Biol. Chem 279, 26, 27294-301, 2004. {PM} {PDF} |
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Expression, crystallization and preliminary crystallographic analysis of YciE, a stress protein from Escherichia coli.
Liu D, Zhao Y, Fan X, Sun Y, Fox RO, Acta Cryst. D 60, Page 1888-9, Oct. 2004. {PM} {PDF} |
2003 ∨ ∧ ⊗ | PubMed 2003 |
 |
The crystal structure of Escherichia coli heat shock protein YedU reveals three potential catalytic active sites,
Yonghong Zhao, Deqian Liu, Warna D. Kaluarachi, Henry D. Beleamy, Mark A. White, and Robert O. Fox, (2003), Protein Science 12, 2303-11, 2003. {PM} {PDF} |
 |
An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution,
Emily E. Scott, You Ai He, Michael R. Webster, Mark A. White, Christopher C. Chin, James R. Halpert, Erik F. Johnson, and C. David Stout, (2003), PNAS 100, 13196-13201, 2003. {PM} {PDF} |
 |
Crystallization and preliminary X-ray diffraction analysis of Langat virus envelope protein domain III,
Mark A. White, Deqian Liu, Michael R. Holbrook, Robert E. Shope, Alan D. T. Barrett and Robert O. Fox, (2003), Acta Cryst. D 59, 1049-51, 2003. {IUCr} {PDF} |
 |
Crystallization and preliminary X-ray diffraction analysis of Jun a 1, the
major allergen isolated from pollen of the mountain cedar Juniperus ashei,
Deqian Liu, Terumi Midoro-Horiuti, Mark A. White, Edward G. Brooks, Randall M. Goldblum and Edmund W. Czerwinski (2003), Acta Cryst. D 59, 1052-53, 2003. {IUCr} {PDF} |
 |
Structural and mechanistic insight from high resolution structures of archaeal rhodopsins.
Landau EM, Pebay-Peyroula E, Neutze R. FEBS Lett. 555(1), Page 51-6. Nov 27, 2003. {PM} {PDF} |
2002 ∨ ∧ ⊗ | PubMed 2002 |
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Early structural rearrangements in the photocycle of an integral membrane sensory receptor.
Edman K, Royant A, Nollert P, Maxwell CA, Pebay-Peyroula E, Navarro J, Neutze R, Landau EM., Structure. 2002 Apr;10(4):473-82. {PM} {PDF} |
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Crystallization of membrane proteins in cubo.,
Nollert P, Navarro J, Landau EM., Methods Enzymol. 2002;343:183-99. {PM} {PDF} |
2001 ∨ ∧ ⊗ | PubMed 2001 |
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Structural and Functional Linkages Between SubunitInterfaces in Mammalian Pyruvate Kinase,
John O. Wooll, Robert H. E. Friesen, Mark A. White, Stanley J. Watowich, Robert O. Fox, J. Ching Lee* and Edmund W. Czerwinski*, (2001), J. Mol. Biol. 312, 525-540, 2001. {PM} {PDF} |
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X-ray structure of sensory rhodopsin II at 2.1-A resolution.
Royant A, Nollert P, Edman K, Neutze R, Landau EM, Pebay-Peyroula E, Navarro J., Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10131-6. Epub 2001 Aug 14. {PM} {PDF} |
2000 ∨ ∧ ⊗ | PubMed 2000 |
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Kinetic and structural characterization of the glutathione-binding site of aldose reductase.,
Dixit BL, Balendiran GK, Watowich SJ, Srivastava S, Ramana KV, Petrash JM, Bhatnagar A, Srivastava SK., J Biol Chem. 2000 Jul 14;275(28):21587-95. {PM} {PDF} |
1999 ∧ ⊗ | PubMed 1999 |
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Calibration of Spiral Readout Image Plate Detectors,
Mark A. White, Stanley J. Watowich, and Robert O. Fox, (1999), J. Appl. Cryst. 32, 65-70, 1999. {IUCr} {PDF} |
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