Publications resulting from Core engagement

70

Morrison EA, Bowerman S, Sylvers KL, Wereszczynski J, Musselman CA. The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome. Elife. 2018 Apr 12;7. pii: e31481. doi: 10.7554/eLife.31481. PubMed PMID: 29648537; PubMed Central PMCID: PMC5953545.

   

69

Cho C, Chande AT, Gakhar L, Hunt J, Ketterer MR, Apicella MA. Characterization of a nontypeable Haemophilus influenzae thermonuclease. PLoS One. 2018 May 10;13(5):e0197010. doi: 10.1371/journal.pone.0197010. eCollection 2018. PubMed PMID: 29746527.

   

68

Kondratick CM, Litman JM, Shaffer KV, Washington MT, Dieckman LM. Crystal structures of PCNA mutant proteins defective in gene silencing suggest a novel interaction site on the front face of the PCNA ring. PLoS One. 2018 Mar 2;13(3):e0193333. doi: 10.1371/journal.pone.0193333. eCollection 2018. PubMed PMID: 29499038.

5V7K - PCNA mutant D41A/D42A Protein Defective in Gene Silencing

5V7L - PCNA mutant R61A/D63A Protein Defective in Gene Silencing

5V7M - PCNA mutant L126A/I128A Protein Defective in Gene Silencing

   

67

Shanmuganatham KK, Wallace RS, Ting-I Lee A, Plapp BV. Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Protein Sci. 2018 Mar;27(3):750-768. doi: 10.1002/pro.3370. Epub 2018 Jan 25. PubMed PMID: 29271062; PubMed Central PMCID: PMC5818739.

5CDG - I220F horse liver alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol

5CDS - I220L horse liver alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol

5CDT - I220V horse liver alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol

5CDU - I220V horse liver alcohol dehydrogenase complexed with NAD and pyrazole

5KJ1 - G173A horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol

5KJ6 - V197I Horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol

5KJC - V222I horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol

5KJE - F322L horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol

5KJF - V222I horse liver alcohol dehydrogenase complexed with NAD+ and trifluoroethanol

   

66

Velez G, Bassuk AG, Schaefer KA, Brooks B, Gakhar L, Mahajan M, Kahn P, Tsang SH, Ferguson PJ, Mahajan VB. A novel de novo CAPN5 mutation in a patient with inflammatory vitreoretinopathy, hearing loss, and developmental delay. Cold Spring Harb Mol Case Stud. 2018 Feb 22. pii: mcs.a002519. doi: 10.1101/mcs.a002519. [Epub ahead of print] PubMed PMID: 29472286.

   

65

Powers KT, Elcock AH, Washington MT. The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility. Nucleic Acids Res. 2018 Jan 29. doi: 10.1093/nar/gky031. [Epub ahead of print] PubMed PMID: 29385534.

   

64

Srivastava D, Razzaghi M, Henzl MT, Dey M. Structural Investigation of a Dimeric Variant of Pyruvate Kinase Muscle Isoform 2. Biochemistry. 2017 Dec 19;56(50):6517-6520. doi: 10.1021/acs.biochem.7b01013. Epub 2017 Dec 1. PubMed PMID: 29182273.

6B6U - Pyruvate Kinase M2 mutant - S437Y

   

63

Vance NR, Gakhar L, Spies MA. Allosteric Tuning of Caspase-7: A Fragment-Based Drug Discovery Approach. Angew Chem Int Ed Engl. 2017 Nov 13;56(46):14443-14447. doi: 10.1002/anie.201706959. Epub 2017 Oct 9. PubMed PMID: 28940929; PubMed Central PMCID: PMC5698726.

5V6U - Crystal structure of human caspase-7 soaked with allosteric inhibitor 2-[(2-acetylphenyl)sulfanyl]benzoic acid

   

62

Schnicker NJ, Razzaghi M, Guha Thakurta S, Chakravarthy S, Dey M. Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu. Biochemistry. 2017 Oct 31;56(43):5771-5785. doi: 10.1021/acs.biochem.7b00601. Epub 2017 Oct 19. PubMed PMID: 28981257; PubMed Central PMCID: PMC5735995.

5V7Y - Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu

   

61

Xu Z, Gakhar L, Bain FE, Spies M, Fuentes EJ. The Tiam1 guanine nucleotide exchange factor is auto-inhibited by its pleckstrin homology coiled-coil extension domain. J Biol Chem. 2017 Oct 27;292(43):17777-17793. Doi: 10.1074/jbc.M117.799114. Epub 2017 Sep 7. PubMed PMID: 28882897; PubMed Central PMCID: PMC5663878.

   

60

Sinn PL, Hwang BY, Li N, Ortiz JLS, Shirazi E, Parekh KR, Cooney AL, Schaffer DV, McCray PB Jr. Novel GP64 envelope variants for improved delivery to human airway epithelial cells. Gene Ther. 2017 Sep 7. doi: 10.1038/gt.2017.78. [Epub ahead of print] PubMed PMID: 28880020.

   

59

Ferraro DJ, Okerlund A, Brown E, Ramaswamy S. One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase. IUCrJ 2017 Sep Volume 4| Part 5| September 2017| ISSN: 2052-2525 https://doi.org/10.1107/S2052252517008223 N1 - doi:10.1107/S2052252517008223

   

58

Yadav RP, Gakhar L, Yu L, Artemyev NO. Unique structural features of the AIPL1-FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness. Proc Natl Acad Sci U S A. 2017 Jul 24. pii: 201704782. doi: 10.1073/pnas.1704782114. [Epub ahead of print] PubMed PMID: 28739921.

5U9A - Crystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)

5U9I - Crystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with S-farnesyl-L-cysteine methyl ester

5U9J - Crystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with geranyl geranyl pyrophoshate

5U9K - Crystal structure of V71F mutant of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)

5V35 - Crystal structure of V71F mutant of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with S-farnesyl-L-cysteine methyl ester

   

57

Plapp BV, Savarimuthu BR, Ferraro DJ, Rubach JK, Brown EN, Ramaswamy S. Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Biochemistry. 2017 Jul 18;56(28):3632-3646. doi: 10.1021/acs.biochem.7b00446. Epub 2017 Jul 7. PubMed PMID: 28640600; PubMed Central PMCID: PMC5518280.

5VN1 - horse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1-methylhexylformamide

5VJ5 - Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline

5VJG - horse liver alcohol dehydrogenase complexed with 2,2'bipyridine

5VKR - Horse liver alcohol dehydrogenase complexed with adenosine-5-diphosphoribose

5VL0 - horse liver alcohol dehydrogenase complexed with NADH and N-benzyformamide

   

56

Schnicker NJ, De Silva SM, Todd JD, Dey M. Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter. Biochemistry. 2017 Jun 13;56(23):2873-2885. Doi: 10.1021/acs.biochem.7b00099. Epub 2017 May 30. PubMed PMID: 28511016.

5TFZ - Crystal structure of the dimethylsulfoniopropionate (DMSP) lyase DddK complexed with nickel and diacrylate

5TG0 - Crystal structure of the dimethylsulfoniopropionate (DMSP) lyase DddK complexed with iron and zinc

   

55

Madison MN, Welch JL, Okeoma CM. Isolation of Exosomes from Semen for in vitro Uptake and HIV-1 Infection Assays. Bio Protoc. 2017 Apr 5;7(7). pii: e2216. doi: 10.21769/BioProtoc.2216. PubMed PMID: 28660234; PubMed Central PMCID: PMC5484154.

   

54

Welch JL, Madison MN, Margolick JB, Galvin S, Gupta P, Martínez-Maza O, Dash C, Okeoma CM. Effect of prolonged freezing of semen on exosome recovery and biologic activity. Sci Rep. 2017 Mar 24;7:45034. doi: 10.1038/srep45034. PubMed PMID: 28338013; PubMed Central PMCID: PMC5364471.

   

53

Ghosh S, Yu CL, Ferraro DJ, Sudha S, Pal SK, Schaefer WF, Gibson DT, Ramaswamy S. Blue protein with red fluorescence. Proc Natl Acad Sci U S A. 2016 Sep 29. pii: 201525622. [Epub ahead of print] PubMed PMID: 27688756.

5F6Z - Sandercyanin Fluorescent Protein purified from Sander vitreus

5EZ2 - Sandercyanin Fluorescent Protein (SFP)

5F1E - Apo protein of Sandercyanin

   

52

Kim K, Plapp BV. Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93. Chem Biol Interact. 2016 Dec 23. pii: S0009-2797(16)30754-2. doi: 10.1016/j.cbi.2016.12.016. [Epub ahead of print] PubMed PMID: 28025168; PubMed Central PMCID: PMC5481492.

5KCZ - horse liver S48T alcohol dehydrogenase complexed with NAD and trifluoroethanol

5KCP - horse liver S48T alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol

   

51

Liu X, Speckhard DC, Shepherd TR, Sun YJ, Hengel SR, Yu L, Fowler CA, Gakhar L, Fuentes EJ. Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions. Structure. 2016 Dec 6;24(12):2053-2066. Doi: 10.1016/j.str.2016.08.019. PubMed PMID: 27998539.

4NXP - Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM)

4NXQ - Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Caspr4 Peptide

4NXR - Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Neurexin-1 Peptide

   

50

Brummett AE, Dey M. New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ. Biochemistry. 2016 Nov 8;55(44):6162-6174. Epub 2016 Oct 28. PubMed PMID: 27755868.

5JSO - Structures of DddQ from Ruegeria lac. Reveal Key Residues for Metal Binding and Catalysis - TRIS bound

5JSP - New Mechanistic Insight from Substrate and Product Bound Structures of the Metal-dependent Dimethylsulfoniopropionate Lyase DddQ

5JSR - New Mechanistic Insight from Substrate and Product Bound Structures of the Metal-dependent Dimethylsulfoniopropionate Lyase DddQ

   

49

Ulland TK, Jain N, Hornick EE, Elliott EI, Clay GM, Sadler JJ, Mills KA, Janowski AM, Volk AP, Wang K, Legge KL, Gakhar L, Bourdi M, Ferguson PJ, Wilson ME, Cassel SL, Sutterwala FS. Nlrp12 mutation causes C57BL/6J strain-specific defect in neutrophil recruitment. Nat Commun. 2016 Oct 25;7:13180. doi:10.1038/ncomms13180. PubMed PMID: 27779193.

   

48

Hastie JL, Williams KB, Bohr LL, Houtman JC, Gakhar L, Ellermeier CD. The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation. PLoS Genet. 2016 Sep 7;12(9):e1006287. doi: 10.1371/journal.pgen.1006287. eCollection 2016 Sep. PubMed PMID: 27602573.

5JEN - Crystal structure of the anti-sigma factor RsiV bound to lysozyme

   

47

Gakhar L, Bassuk AG, Velez G, Khan S, Yang J, Tsang SH, Mahajan VB. Small-angle X-ray scattering of calpain-5 reveals a highly open conformation among calpains. J Struct Biol. 2016 Jul 27. pii: S1047-8477(16)30158-7. doi: 10.1016/j.jsb.2016.07.017. [Epub ahead of print] PubMed PMID: 27474374.

   

46

Schnicker NJ, Dey M. Bacillus anthracis Prolyl 4-Hydroxylase Modifies Collagen-like Substrates in Asymmetric Patterns. J Biol Chem. 2016 Jun 17;291(25):13360-74. doi: 10.1074/jbc.M116.725432. Epub 2016 Apr 21. PubMed PMID: 27129244; PubMed Central PMCID: PMC4933245.

5IAT - Mechanistic and Structural Analysis of Substrate Recognition and Cofactor Binding by an Unusual Bacterial Prolyl Hydroxylase - apo-BaP4H

5IAV - Mechanistic and Structural Analysis of Substrate Recognition and Cofactor Binding by an Unusual Bacterial Prolyl Hydroxylase - Co-BaP4H-MLI

5IAX - Mechanistic and Structural Analysis of Substrate Recognition and Cofactor Binding by an Unusual Bacterial Prolyl Hydroxylase - Co-BaP4H-PPG

   

45

Guo Q, Gakhar L, Wickersham K, Francis K, Vardi-Kilshtain A, Major DT, Cheatum CM, Kohen A. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii. Biochemistry. 2016 May 17;55(19):2760-71. Doi: 10.1021/acs.biochem.6b00181. Epub 2016 May 3. PubMed PMID: 27100912; PubMed Central PMCID: PMC4917879.

5DN9 - Crystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azide

5DNA - Crystal structure of Candida boidinii formate dehydrogenase

   

44

Schnicker NJ, Dey M. Structural analysis of cofactor binding for a prolyl 4-hydroxylase from the pathogenic bacterium Bacillus anthracis. Acta Crystallogr D Struct Biol. 2016 May;72(Pt 5):675-81. doi: 10.1107/S2059798316004198. Epub 2016 Apr 26. PubMed PMID: 27139630.

5HV4 - Crystal Structure of a Prolyl 4-Hydroxylase Complexed with Alpha-ketoglutarate from the Pathogenic Bacterium Bacillus anthracis in C2221

   

43

Yadav RP, Majumder A, Gakhar L, Artemyev NO. Extended conformation of the proline-rich domain of human aryl hydrocarbon receptor-interacting protein-like 1: implications for retina disease. J Neurochem. 2015 Oct;135(1):165-75. doi: 10.1111/jnc.13223. Epub 2015 Aug 25. PubMed PMID: 26139345.

   

42

Wert KJ, Bassuk AG, Wu WH, Gakhar L, Coglan D, Mahajan M, Wu S, Yang J, Lin CS, Tsang SH, Mahajan VB. CAPN5 mutation in hereditary uveitis: the R243L mutation increases calpain catalytic activity and triggers intraocular inflammation in a mouse model. Hum Mol Genet. 2015 Aug 15;24(16):4584-98. doi: 10.1093/hmg/ddv189. Epub 2015 May 20. PubMed PMID: 25994508; PubMed Central PMCID: PMC4512628.

   

41

LuCore SD, Litman JM, Powers KT, Gao S, Lynn AM, Tollefson WT, Fenn TD, Washington MT, Schnieders MJ. Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. Biophys J. 2015 Aug 18;109(4):816-26. Doi: 10.1016/j.bpj.2015.06.062. PubMed PMID: 26287633; PubMed Central PMCID: PMC4547145.

   

40

Feldkamp MD, Gakhar L, Pandey N, Shea MA. Opposing orientations of the anti-psychotic drug trifluoperazine selected by alternate conformations of M144 in calmodulin. Proteins. 2015 May;83(5):989-96. doi: 10.1002/prot.24781. Epub 2015 Mar 25. PubMed PMID: 25694384; PubMed Central PMCID: PMC4400249.

4RJD - TFP bound in alternate orientations to calcium-saturated Calmodulin C-Domains

   

39

Jagodinsky JC, Akgun U. Characterizing the binding interactions between P-glycoprotein and eight known cardiovascular transport substrates. Pharmacol Res Perspect. 2015 Mar;3(2):e00114. doi: 10.1002/prp2.114. PubMed PMID: 25729581; PubMed Central PMCID: PMC4324688.

   

38

Cho C, Chande A, Gakhar L, Bakaletz LO, Jurcisek JA, Ketterer M, Shao J, Gotoh K, Foster E, Hunt J, O'Brien E, Apicella MA. Role of the nuclease of nontypeable Haemophilus influenzae in dispersal of organisms from biofilms. Infect Immun. 2015 Mar;83(3):950-7. doi: 10.1128/IAI.02601-14. Epub 2014 Dec 29. PubMed PMID: 25547799; PubMed Central PMCID: PMC4333478.

   

37

Cheguru P, Majumder A, Yadav R, Gopalakrishna KN, Gakhar L, Artemyev NO. The solution structure of the transducin-α-uncoordinated 119 protein complex suggests occlusion of the Gβ₁γ₁-binding sites. FEBS J. 2015 Feb;282(3):550-61. doi: 10.1111/febs.13161. Epub 2014 Dec 12. PubMed PMID: 25425538; PubMed Central PMCID: PMC4310827.

   

36

Doron D, Stojković V, Gakhar L, Vardi-Kilshtain A, Kohen A, Major DT. Free energy simulations of active-site mutants of dihydrofolate reductase. J Phys Chem B. 2015 Jan 22;119(3):906-16. doi: 10.1021/jp5059963. Epub 2014 Nov 21. PubMed PMID: 25382260.

4QLE - Crystal structure of I14A DHFR mutant complexed with folate and NADP+

4QLF - Crystal structure of I14G DHFR mutant complexed with folate and NADP+

4QLG - Crystal structure of I14V DHFR mutant complexed with folate and NADP+

   

35

Bassuk AG, Yeh S, Wu S, Martin DF, Tsang SH, Gakhar L, Mahajan VB. Structural modeling of a novel CAPN5 mutation that causes uveitis and neovascular retinal detachment. PLoS One. 2015 Apr 9;10(4):e0122352. doi: 10.1371/journal.pone.0122352. eCollection 2015. PubMed PMID: 25856303; PubMed Central PMCID: PMC4391918.

   

34

Streeter J, Schickling BM, Jiang S, Stanic B, Thiel WH, Gakhar L, Houtman JC, Miller FJ Jr. Phosphorylation of Nox1 regulates association with NoxA1 activation domain. Circ Res. 2014 Nov 7;115(11):911-8. doi: 10.1161/CIRCRESAHA.115.304267. Epub 2014 Sep 16. PubMed PMID: 25228390.

   

33

Raj SB, Ramaswamy S, Plapp BV. Yeast alcohol dehydrogenase structure and catalysis. Biochemistry. 2014 Sep 16;53(36):5791-803. doi: 10.1021/bi5006442. Epub 2014 Sep 3. PubMed PMID: 25157460; PubMed Central PMCID: PMC4165444.

   

32

Ver Heul AM, Gakhar L, Piper RC, Subramanian R. Crystal structure of a complex of NOD1 CARD and ubiquitin. PLoS One. 2014 Aug 15;9(8):e104017. doi: 10.1371/journal.pone.0104017. eCollection 2014. PubMed PMID: 25127239; PubMed Central PMCID: PMC4134136.

4JQW - Crystal Structure of a Complex of NOD1 CARD and Ubiquitin

   

31

Yahashiri A, Rubach JK, Plapp BV. Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis. Biochemistry. 2014 Feb 11;53(5):881-94. doi: 10.1021/bi401583f. Epub 2014 Jan 30. PubMed PMID: 24437493; PubMed Central PMCID: PMC3969020.

   

30

Dieckman LM, Boehm EM, Hingorani MM, Washington MT. Distinct structural alterations in proliferating cell nuclear antigen block DNA mismatch repair. Biochemistry. 2013 Aug 20;52(33):5611-9. doi: 10.1021/bi400378e. Epub 2013 Aug 2. PubMed PMID: 23869605; PubMed Central PMCID: PMC3845532.

   

29

Darbro BW, Mahajan VB, Gakhar L, Skeie JM, Campbell E, Wu S, Bing X, Millen KJ, Dobyns WB, Kessler JA, Jalali A, Cremer J, Segre A, Manak JR, Aldinger KA, Suzuki S, Natsume N, Ono M, Hai HD, Viet le T, Loddo S, Valente EM, Bernardini L, Ghonge N, Ferguson PJ, Bassuk AG. Mutations in extracellular matrix genes NID1 and LAMC1 cause autosomal dominant Dandy-Walker malformation and occipital cephaloceles. Hum Mutat. 2013 Aug;34(8):1075-9. doi: 10.1002/humu.22351. Epub 2013 May 28. PubMed PMID: 23674478; PubMed Central PMCID: PMC3714376.

   

28

Majumder A, Gopalakrishna KN, Cheguru P, Gakhar L, Artemyev NO. Interaction of aryl hydrocarbon receptor-interacting protein-like 1 with the farnesyl moiety. J Biol Chem. 2013 Jul 19;288(29):21320-8. doi: 10.1074/jbc.M113.476242. Epub 2013 Jun 4. PubMed PMID: 23737531; PubMed Central PMCID: PMC3774400.

   

27

Joshi M, Gakhar L, Fuentes EJ. High-resolution structure of the Tiam1 PHn-CC-Ex domain. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jul;69(Pt 7):744-52. doi: 10.1107/S1744309113014206. Epub 2013 Jun 27. PubMed PMID: 23832200; PubMed Central PMCID: PMC3702317.

4K2O - The Structure of a Triple Mutant of the Tiam1 PH-CC-Ex Domain

4K2P - The Structure of a Quintuple Mutant of the Tiam1 PH-CC-Ex Domain

   

26

Pashkova N, Gakhar L, Winistorfer SC, Sunshine AB, Rich M, Dunham MJ, Yu L, Piper RC. The yeast Alix homolog Bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes. Dev Cell. 2013 Jun 10;25(5):520-33. doi: 10.1016/j.devcel.2013.04.007. Epub 2013 May 30. PubMed PMID: 23726974; PubMed Central PMCID: PMC3755756.

4JIO - Bro1 V domain and ubiquitin

4JJY - Alix V domain

   

25

Liu Y, Bartlett JA, Di ME, Bomberger JM, Chan YR, Gakhar L, Mallampalli RK, McCray PB Jr, Di YP. SPLUNC1/BPIFA1 contributes to pulmonary host defense against Klebsiella pneumoniae respiratory infection. Am J Pathol. 2013 May;182(5):1519-31. doi: 10.1016/j.ajpath.2013.01.050. Epub 2013 Mar 15. PubMed PMID: 23499554; PubMed Central PMCID: PMC3644735.

   

24

Liu X, Shepherd TR, Murray AM, Xu Z, Fuentes EJ. The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics. Structure. 2013 Mar 5;21(3):342-54. Doi: 10.1016/j.str.2013.01.004. Epub 2013 Feb 7. PubMed PMID: 23395182; PubMed Central PMCID: PMC4086710.

4GVC - Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with phosphorylated Syndecan1 Peptide

4GVD - Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with Syndecan1 Peptide

   

23

Pryor JM, Gakhar L, Washington MT. Structure and functional analysis of the BRCT domain of translesion synthesis DNA polymerase Rev1. Biochemistry. 2013 Jan 8;52(1):254-63. doi: 10.1021/bi301572z. Epub 2012 Dec 20. PubMed PMID: 23240687; PubMed Central PMCID: PMC3580236.

4ID3 - Crystal Structure of the BRCT domain of S. Cerevisiae Rev1

   

22

Chen L, Lin YL, Peng G, Li F. Structural basis for multifunctional roles of mammalian aminopeptidase N. Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17966-71. doi: 10.1073/pnas.1210123109. Epub 2012 Oct 15. PubMed PMID: 23071329; PubMed Central PMCID: PMC3497818.

   

21

Mohanty SK, Yu CL, Das S, Louie TM, Gakhar L, Subramanian M. Delineation of the caffeine C-8 oxidation pathway in Pseudomonas sp. strain CBB1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism. J Bacteriol. 2012 Aug;194(15):3872-82. Doi: 10.1128/JB.00597-12. Epub 2012 May 18. PubMed PMID: 22609920; PubMed Central PMCID: PMC3416557.

   

20

Plapp BV, Ramaswamy S. Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Biochemistry. 2012 May 15;51(19):4035-48. doi: 10.1021/bi300378n. Epub 2012 May 1. PubMed PMID: 22531044; PubMed Central PMCID: PMC3352959.

   

19

Summers RM, Louie TM, Yu CL, Gakhar L, Louie KC, Subramanian M. Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids. J Bacteriol. 2012 Apr;194(8):2041-9. doi: 10.1128/JB.06637-11. Epub 2012 Feb 10. PubMed PMID: 22328667; PubMed Central PMCID: PMC3318484.

   

18

Kohlgraf KG, Ackermann AR, Burnell KK, Srikantha RN, Joly SA, Bartlett JA, Gakhar L, Johnson GK, McCray PB Jr, Guthmiller JM, Brogden KA. Quantitation of SPLUNC1 in saliva with an xMAP particle-based antibody capture and detection immunoassay. Arch Oral Biol. 2012 Feb;57(2):197-204. Doi: 10.1016/j.archoralbio.2011.08.013. Epub 2011 Sep 16. PubMed PMID: 21925642; PubMed Central PMCID: PMC3260398.

   

17

Mahajan VB, Skeie JM, Bassuk AG, Fingert JH, Braun TA, Daggett HT, Folk JC, Sheffield VC, Stone EM. Calpain-5 mutations cause autoimmune uveitis, retinal neovascularization, and photoreceptor degeneration. PLoS Genet. 2012;8(10):e1003001. doi: 10.1371/journal.pgen.1003001. Epub 2012 Oct 4. PubMed PMID: 23055945; PubMed Central PMCID: PMC3464205.

   

16

Kavanaugh JS, Gakhar L, Horswill AR. The structure of LsrB from Yersinia pestis complexed with autoinducer-2. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Dec 1;67(Pt 12):1501-5. doi: 10.1107/S1744309111042953. Epub 2011 Nov 29. PubMed PMID: 22139152; PubMed Central PMCID: PMC3232125.

3T95 - Crystal structure of LsrB from Yersinia pestis complexed with autoinducer-2

   

15

Tsutakawa SE, Van Wynsberghe AW, Freudenthal BD, Weinacht CP, Gakhar L, Washington MT, Zhuang Z, Tainer JA, Ivanov I. Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17672-7. doi: 10.1073/pnas.1110480108. Epub 2011 Oct 17. PubMed PMID: 22006297; PubMed Central PMCID: PMC3203759.

   

14

Bartlett JA, Gakhar L, Penterman J, Singh PK, Mallampalli RK, Porter E, McCray PB Jr. PLUNC: a multifunctional surfactant of the airways. Biochem Soc Trans. 2011 Aug;39(4):1012-6. doi: 10.1042/BST0391012. Erratum in: Biochem Soc Trans. 2011 Oct;39(5):1549. Bartlett, Jennifer [corrected to Bartlett, Jennifer A]; Singh, Pradeep [corrected to Singh, Pradeep K]. PubMed PMID: 21787339; PubMed Central PMCID: PMC3572202.

   

13

Freudenthal BD, Brogie JE, Gakhar L, Kondratick CM, Washington MT. Crystal structure of SUMO-modified proliferating cell nuclear antigen. J Mol Biol. 2011 Feb 11;406(1):9-17. doi: 10.1016/j.jmb.2010.12.015. Epub 2010 Dec 15. PubMed PMID: 21167178; PubMed Central PMCID: PMC3193175.

3PGE - Structure of sumoylated PCNA

   

12

Pashkova N, Gakhar L, Winistorfer SC, Yu L, Ramaswamy S, Piper RC. WD40 repeat propellers define a ubiquitin-binding domain that regulates turnover of F box proteins. Mol Cell. 2010 Nov 12;40(3):433-43. Doi: 10.1016/j.molcel.2010.10.018. PubMed PMID: 21070969; PubMed Central PMCID: PMC3266742.

3ODT - Crystal structure of WD40 beta propeller domain of Doa1

   

11

Ray NB, Durairaj L, Chen BB, McVerry BJ, Ryan AJ, Donahoe M, Waltenbaugh AK, O'Donnell CP, Henderson FC, Etscheidt CA, McCoy DM, Agassandian M, Hayes-Rowan EC, Coon TA, Butler PL, Gakhar L, Mathur SN, Sieren JC, Tyurina YY, Kagan VE, McLennan G, Mallampalli RK. Dynamic regulation of cardiolipin by the lipid pump Atp8b1 determines the severity of lung injury in experimental pneumonia. Nat Med. 2010 Oct;16(10):1120-7. doi: 10.1038/nm.2213. Epub 2010 Sep 19. PubMed PMID: 20852622; PubMed Central PMCID: PMC4500192.

   

10

Hass CS, Gakhar L, Wold MS. Functional characterization of a cancer causing mutation in human replication protein A. Mol Cancer Res. 2010 Jul;8(7):1017-26. doi: 10.1158/1541-7786.MCR-10-0161. Epub 2010 Jun 29. PubMed PMID: 20587534; PubMed Central PMCID: PMC2905489.

   

9

Shepherd TR, Klaus SM, Liu X, Ramaswamy S, DeMali KA, Fuentes EJ. The Tiam1 PDZ domain couples to Syndecan1 and promotes cell-matrix adhesion. J Mol Biol. 2010 May 21;398(5):730-46. doi: 10.1016/j.jmb.2010.03.047. Epub 2010 Mar 31. PubMed PMID: 20361982.

3KZD - Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain

3KZE - Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in Complex With SSRKEYYA Peptide

   

8

Freudenthal BD, Gakhar L, Ramaswamy S, Washington MT. Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange. Nat Struct Mol Biol. 2010 Apr;17(4):479-84. Doi: 10.1038/nsmb.1776. Epub 2010 Mar 21. PubMed PMID: 20305653; PubMed Central PMCID: PMC2920209.

3L0W - Structure of split monoubiquitinated PCNA with ubiquitin in position two

3L0X - Structure of split yeast PCNA

3L10 - Structure of split monoubiquitinated PCNA with ubiquitin in position one

   

7

Gakhar L, Bartlett JA, Penterman J, Mizrachi D, Singh PK, Mallampalli RK, Ramaswamy S, McCray PB Jr. PLUNC is a novel airway surfactant protein with anti-biofilm activity. PLoS One. 2010 Feb 9;5(2):e9098. Doi: 10.1371/journal.pone.0009098. PubMed PMID: 20161732; PubMed Central PMCID: PMC2817724.

   

6

Barren B, Gakhar L, Muradov H, Boyd KK, Ramaswamy S, Artemyev NO. Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit. EMBO J. 2009 Nov 18;28(22):3613-22. doi: 10.1038/emboj.2009.284. Epub 2009 Oct 1. PubMed PMID: 19798052; PubMed Central PMCID: PMC2782096.

3JWQ - Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with

sildenafil

3JWR - Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with 3-isobutyl-1-methylxanthine (IBMX) and PDE6 gamma-subunit inhibitory peptide 70-87

   

5

Jia HP, Look DC, Tan P, Shi L, Hickey M, Gakhar L, Chappell MC, Wohlford-Lenane C, McCray PB Jr. Ectodomain shedding of angiotensin converting enzyme 2 in human airway epithelia. Am J Physiol Lung Cell Mol Physiol. 2009 Jul;297(1):L84-96. doi: 10.1152/ajplung.00071.2009. Epub 2009 May 1. PubMed PMID: 19411314; PubMed Central PMCID: PMC2711803.

   

4

Freudenthal BD, Gakhar L, Ramaswamy S, Washington MT. A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactions. Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):560-6. doi: 10.1107/S0907444909011329. Epub 2009 May 15. PubMed PMID: 19465770; PubMed Central PMCID: PMC2685733.

3GPM - Structure of the trimeric form of the E113G PCNA mutant protein

3GPN - Structure of the non-trimeric form of the E113G PCNA mutant protein

   

3

Little HJ, Rorick NK, Su LI, Baldock C, Malhotra S, Jowitt T, Gakhar L, Subramanian R, Schutte BC, Dixon MJ, Shore P. Missense mutations that cause Van der Woude syndrome and popliteal pterygium syndrome affect the DNA-binding and transcriptional activation functions of IRF6. Hum Mol Genet. 2009 Feb 1;18(3):535-45. doi: 10.1093/hmg/ddn381. Epub 2008 Nov 26. Erratum in: Hum Mol Genet.2009 Apr 15;18(8):1544. PubMed PMID: 19036739; PubMed Central PMCID: PMC2638798.

   

2

Freudenthal BD, Ramaswamy S, Hingorani MM, Washington MT. Structure of a mutant form of proliferating cell nuclear antigen that blocks translesion DNA synthesis. Biochemistry. 2008 Dec 16;47(50):13354-61. doi: 10.1021/bi8017762. PubMed PMID: 19053247; PubMed Central PMCID: PMC2703463.

   

1

Ataman ZA, Gakhar L, Sorensen BR, Hell JW, Shea MA. The NMDA receptor NR1 C1 region bound to calmodulin: structural insights into functional differences between homologous domains. Structure. 2007 Dec;15(12):1603-17. PubMed PMID: 18073110; PubMed Central PMCID: PMC2246159.

2HQW - Crystal Structure of Ca2+/Calmodulin bound to NMDA Receptor NR1C1 peptide