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Lokesh Gakhar, Ph.D. - Publications

Affiliations: 
2003 University of Iowa, Iowa City, IA 
Area:
Structural Biology
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65 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Honda M, Razzaghi M, Gaur P, Malacaria E, Di Biagi L, Aiello FA, Paintsil EA, Stanfield A, Deppe BJ, Gakhar L, Schnicker NJ, Spies MA, Pichierri P, Spies M. Human RAD52 double-ring remodels replication forks restricting fork reversal. Biorxiv : the Preprint Server For Biology. PMID 38014173 DOI: 10.1101/2023.11.14.566657  0.529
2023 Sandouk A, Xu Z, Baruah S, Tremblay M, Hopkins JB, Chakravarthy S, Gakhar L, Schnicker NJ, Houtman JCD. GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production. Scientific Reports. 13: 3505. PMID 36864087 DOI: 10.1038/s41598-023-30562-7  0.3
2022 Plapp BV, Gakhar L, Subramanian R. Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase. Acta Crystallographica. Section D, Structural Biology. 78: 1221-1234. PMID 36189742 DOI: 10.1107/S2059798322008361  0.674
2022 Weaver TM, Hoitsma NM, Spencer JJ, Gakhar L, Schnicker NJ, Freudenthal BD. Structural basis for APE1 processing DNA damage in the nucleosome. Nature Communications. 13: 5390. PMID 36104361 DOI: 10.1038/s41467-022-33057-7  0.605
2021 Pashkova N, Gakhar L, Yu L, Schnicker NJ, Minard AY, Winistorfer S, Johnson IE, Piper RC. ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals. Elife. 10. PMID 34821552 DOI: 10.7554/eLife.72583  0.599
2021 Pashkova N, Yu L, Schnicker NJ, Tseng CC, Gakhar L, Katzmann DJ, Piper RC. Interactions of ubiquitin and CHMP5 with the V domain of HD-PTP reveals role for regulation of Vps4 ATPase. Molecular Biology of the Cell. mbcE21040219. PMID 34586919 DOI: 10.1091/mbc.E21-04-0219  0.588
2020 Beattie SR, Schnicker NJ, Murante T, Kettimuthu K, Williams NS, Gakhar L, Krysan D. Benzothiourea derivates target the secretory pathway of the human fungal pathogen Cryptococcus neoformans. Acs Infectious Diseases. PMID 32070095 DOI: 10.1021/Acsinfecdis.9B00478  0.596
2020 Velez G, Sun YJ, Khan S, Yang J, Herrmann J, Chemudupati T, MacLaren RE, Gakhar L, Wakatsuki S, Bassuk AG, Mahajan VB. Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants. Cell Reports. 30: 881-892.e5. PMID 31968260 DOI: 10.1016/J.Celrep.2019.12.077  0.695
2019 Pagano P, Guo Q, Ranasinghe C, Schroeder E, Robben K, Häse F, Ye H, Wickersham K, Aspuru-Guzik A, Major DT, Gakhar L, Kohen A, Cheatum CM. Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase. Acs Catalysis. 9: 11199-11206. PMID 33996196 DOI: 10.1021/acscatal.9b03345  0.525
2019 Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR. Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway. Nature Communications. 10: 4127. PMID 31511507 DOI: 10.1038/S41467-019-11931-1  0.371
2019 Srivastava D, Gakhar L, Artemyev NO. Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor. Nature Communications. 10: 3084. PMID 31300652 DOI: 10.1038/s41467-019-11088-x  0.637
2019 Srivastava D, Gakhar L, Artemyev NO. Structural underpinnings of Ric8A function as a G-protein alpha-subunit chaperone and guanine-nucleotide exchange factor. Nature Communications. 10: 3084-3084. DOI: 10.2210/Pdb6N84/Pdb  0.673
2019 Pagano P, Guo Q, Ranasinghe C, Schroeder E, Robben K, Häse F, Ye H, Wickersham K, Aspuru-Guzik A, Major DT, Gakhar L, Kohen A, Cheatum CM. Oscillatory Active-Site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase Acs Catalysis. 9: 11199-11206. DOI: 10.1021/Acscatal.9B03345  0.572
2018 Li Q, Gakhar L, Ashley Spies M. Determinants of human Glucokinase activation and implications for small molecule allosteric control. Biochimica Et Biophysica Acta. PMID 29885360 DOI: 10.1016/J.Bbagen.2018.06.001  0.342
2018 Cho C, Chande AT, Gakhar L, Hunt J, Ketterer MR, Apicella MA. Characterization of a nontypeable Haemophilus influenzae thermonuclease. Plos One. 13: e0197010. PMID 29746527 DOI: 10.1371/Journal.Pone.0197010  0.561
2018 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 Harbor Molecular Case Studies. PMID 29472286 DOI: 10.1101/mcs.a002519  0.637
2018 Joo Sun Y, Hou T, Gakhar L, Awadia S, Garcia-Mata R, Fuentes E. Rational Design of PDZ Domain Specificity Biophysical Journal. 114: 410a. DOI: 10.1016/J.Bpj.2017.11.2270  0.655
2017 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. The Journal of Biological Chemistry. PMID 28882897 DOI: 10.1074/Jbc.M117.799114  0.762
2017 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 28739921 DOI: 10.1073/Pnas.1704782114  0.698
2017 Velez G, Gakhar L, Khan S, Koster HJ, Yang J, Tsang SH, Bassuk AG, Mahajan VB. Crystal structure of the human calpain-5 catalytic core Acta Crystallographica Section a Foundations and Advances. 73: a31-a32. DOI: 10.1107/S0108767317099688  0.678
2016 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 (London, England : 1993). 24: 2053-2066. PMID 27998539 DOI: 10.1016/J.Str.2016.08.019  0.7
2016 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 Genetics. 12: e1006287. PMID 27602573 DOI: 10.1371/Journal.Pgen.1006287  0.799
2016 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. Journal of Structural Biology. PMID 27474374 DOI: 10.1016/J.Jsb.2016.07.017  0.732
2016 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. PMID 27100912 DOI: 10.1021/Acs.Biochem.6B00181  0.588
2016 Mahling R, Fowler CA, Hovey L, Yu L, Gakhar L, Lin Z, Pandey N, Martins T, Shea MA. Structural Differences in Calmodulin Bound to Voltagate-Gated Sodium Channel IQ Motifs Biophysical Journal. 110: 109a. DOI: 10.1016/J.Bpj.2015.11.646  0.671
2016 Joo Sun Y, Hou T, Liu X, Gakhar L, Fuentes E. Structural and Biochemical Characterization of CASK PDZ Interaction with Protein and Lipid Binding Partners Biophysical Journal. 110: 42a. DOI: 10.1016/J.Bpj.2015.11.296  0.718
2016 Fuentes EJ, Liu X, Speckhard DC, Shepherd TR, Hengel SR, Liping L, Fowler CA, Gakhar L. Conformational Dynamics and Structure Underlie the Novel Ligand Binding Specificity of a Tiam1 PDZ Domain Mutant Biophysical Journal. 110: 514a. DOI: 10.1016/J.Bpj.2015.11.2749  0.725
2016 Xu Z, Gakhar L, Boehm E, Washington T, Spies M, Fuentes EJ. Insights into the Autoinhibition Mechanism of the Tiam1 Guanine Nucleotide Exchange Factor Biophysical Journal. 110: 206a. DOI: 10.1016/J.Bpj.2015.11.1149  0.774
2015 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. Journal of Neurochemistry. 135: 165-75. PMID 26139345 DOI: 10.1111/Jnc.13223  0.667
2015 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. Human Molecular Genetics. 24: 4584-98. PMID 25994508 DOI: 10.1093/Hmg/Ddv189  0.682
2015 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. 10: e0122352. PMID 25856303 DOI: 10.1371/Journal.Pone.0122352  0.689
2015 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. 83: 989-96. PMID 25694384 DOI: 10.1002/Prot.24781  0.775
2015 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. Infection and Immunity. 83: 950-7. PMID 25547799 DOI: 10.1128/Iai.02601-14  0.488
2015 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. The Febs Journal. 282: 550-61. PMID 25425538 DOI: 10.1111/Febs.13161  0.66
2015 Doron D, Stojkovi? V, Gakhar L, Vardi-Kilshtain A, Kohen A, Major DT. Free energy simulations of active-site mutants of dihydrofolate reductase. The Journal of Physical Chemistry. B. 119: 906-16. PMID 25382260 DOI: 10.1021/Jp5059963  0.591
2015 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 Human Molecular Genetics. 24: 4584-4598. DOI: 10.1093/hmg/ddv189  0.644
2014 Streeter J, Schickling BM, Jiang S, Stanic B, Thiel WH, Gakhar L, Houtman JC, Miller FJ. Phosphorylation of Nox1 regulates association with NoxA1 activation domain. Circulation Research. 115: 911-8. PMID 25228390 DOI: 10.1161/Circresaha.115.304267  0.662
2014 Ver Heul AM, Gakhar L, Piper RC, Subramanian R. Crystal structure of a complex of NOD1 CARD and ubiquitin. Plos One. 9: e104017. PMID 25127239 DOI: 10.1371/Journal.Pone.0104017  0.777
2013 Joshi M, Gakhar L, Fuentes EJ. High-resolution structure of the Tiam1 PHn-CC-Ex domain. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 69: 744-52. PMID 23832200 DOI: 10.1107/S1744309113014206  0.727
2013 Majumder A, Gopalakrishna KN, Cheguru P, Gakhar L, Artemyev NO. Interaction of aryl hydrocarbon receptor-interacting protein-like 1 with the farnesyl moiety. The Journal of Biological Chemistry. 288: 21320-8. PMID 23737531 DOI: 10.1074/Jbc.M113.476242  0.695
2013 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. Developmental Cell. 25: 520-33. PMID 23726974 DOI: 10.1016/J.Devcel.2013.04.007  0.621
2013 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, et al. Mutations in extracellular matrix genes NID1 and LAMC1 cause autosomal dominant Dandy-Walker malformation and occipital cephaloceles. Human Mutation. 34: 1075-9. PMID 23674478 DOI: 10.1002/Humu.22351  0.686
2013 Liu Y, Bartlett JA, Di ME, Bomberger JM, Chan YR, Gakhar L, Mallampalli RK, McCray PB, Di YP. SPLUNC1/BPIFA1 contributes to pulmonary host defense against Klebsiella pneumoniae respiratory infection. The American Journal of Pathology. 182: 1519-31. PMID 23499554 DOI: 10.1016/J.Ajpath.2013.01.050  0.659
2013 Pryor JM, Gakhar L, Washington MT. Structure and functional analysis of the BRCT domain of translesion synthesis DNA polymerase Rev1. Biochemistry. 52: 254-63. PMID 23240687 DOI: 10.1021/Bi301572Z  0.658
2012 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. Journal of Bacteriology. 194: 3872-82. PMID 22609920 DOI: 10.1128/Jb.00597-12  0.659
2012 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. Journal of Bacteriology. 194: 2041-9. PMID 22328667 DOI: 10.1128/Jb.06637-11  0.718
2012 Kohlgraf KG, Ackermann AR, Burnell KK, Srikantha RN, Joly SA, Bartlett JA, Gakhar L, Johnson GK, McCray PB, Guthmiller JM, Brogden KA. Quantitation of SPLUNC1 in saliva with an xMAP particle-based antibody capture and detection immunoassay. Archives of Oral Biology. 57: 197-204. PMID 21925642 DOI: 10.1016/J.Archoralbio.2011.08.013  0.623
2011 Kavanaugh JS, Gakhar L, Horswill AR. The structure of LsrB from Yersinia pestis complexed with autoinducer-2. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 67: 1501-5. PMID 22139152 DOI: 10.1107/S1744309111042953  0.346
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: 17672-7. PMID 22006297 DOI: 10.1073/Pnas.1110480108  0.79
2011 Bartlett JA, Bartlett J, Gakhar L, Penterman J, Singh PK, Singh P, Mallampalli RK, Porter E, McCray PB. PLUNC: a multifunctional surfactant of the airways. Biochemical Society Transactions. 39: 1012-6. PMID 21787339 DOI: 10.1042/Bst0391012  0.678
2011 Freudenthal BD, Brogie JE, Gakhar L, Kondratick CM, Washington MT. Crystal structure of SUMO-modified proliferating cell nuclear antigen. Journal of Molecular Biology. 406: 9-17. PMID 21167178 DOI: 10.1016/J.Jmb.2010.12.015  0.746
2010 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. Molecular Cell. 40: 433-43. PMID 21070969 DOI: 10.1016/J.Molcel.2010.10.018  0.625
2010 Hass CS, Gakhar L, Wold MS. Functional characterization of a cancer causing mutation in human replication protein A. Molecular Cancer Research : McR. 8: 1017-26. PMID 20587534 DOI: 10.1158/1541-7786.Mcr-10-0161  0.376
2010 Freudenthal BD, Gakhar L, Ramaswamy S, Washington MT. Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange. Nature Structural & Molecular Biology. 17: 479-84. PMID 20305653 DOI: 10.1038/Nsmb.1776  0.748
2010 Gakhar L, Bartlett JA, Penterman J, Mizrachi D, Singh PK, Mallampalli RK, Ramaswamy S, McCray PB. PLUNC is a novel airway surfactant protein with anti-biofilm activity. Plos One. 5: e9098. PMID 20161732 DOI: 10.1371/Journal.Pone.0009098  0.682
2009 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. The Embo Journal. 28: 3613-22. PMID 19798052 DOI: 10.1038/Emboj.2009.284  0.658
2009 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 Crystallographica. Section D, Biological Crystallography. 65: 560-6. PMID 19465770 DOI: 10.1107/S0907444909011329  0.765
2009 Jia HP, Look DC, Tan P, Shi L, Hickey M, Gakhar L, Chappell MC, Wohlford-Lenane C, McCray PB. Ectodomain shedding of angiotensin converting enzyme 2 in human airway epithelia. American Journal of Physiology. Lung Cellular and Molecular Physiology. 297: L84-96. PMID 19411314 DOI: 10.1152/Ajplung.00071.2009  0.578
2009 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. Human Molecular Genetics. 18: 535-45. PMID 19036739 DOI: 10.1093/Hmg/Ddn381  0.742
2009 Little HJ, Rorick NK, Su LI, Baldock C, Malhotra S, Jowitt T, Gakhar L, Subramanian R, Schutte BC, Dixon MJ, Shore P. Erratum: Missense mutations that cause Van der Woude syndrome and popliteal pterygium syndrome affect the DNA-binding and transcriptional activation functions of IRF6 (Human Molecular Genetics (2009) vol. 18(3) (535-545) 10.1093/hmg/ddn381) Human Molecular Genetics. 18. DOI: 10.1093/Hmg/Ddp056  0.695
2007 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 (London, England : 1993). 15: 1603-17. PMID 18073110 DOI: 10.1016/J.Str.2007.10.012  0.683
2005 Gakhar L, Malik ZA, Allen CC, Lipscomb DA, Larkin MJ, Ramaswamy S. Structure and increased thermostability of Rhodococcus sp. naphthalene 1,2-dioxygenase. Journal of Bacteriology. 187: 7222-31. PMID 16237006 DOI: 10.1128/Jb.187.21.7222-7231.2005  0.31
2005 Ferraro DJ, Gakhar L, Ramaswamy S. Rieske business: structure-function of Rieske non-heme oxygenases. Biochemical and Biophysical Research Communications. 338: 175-90. PMID 16168954 DOI: 10.1016/J.Bbrc.2005.08.222  0.726
2005 Gakhar L, Wiencek JM. A possible additional role of mineral oil in successful flash cooling Journal of Applied Crystallography. 38: 945-950. DOI: 10.1107/S0021889805028049  0.661
2002 Malik ZA, Allen CC, Gakhar L, Lipscomb DA, Larkin MJ, Ramaswamy S. Crystallization and preliminary X-ray diffraction analysis of naphthalene dioxygenase from Rhodococcus sp. strain NCIMB 12038. Acta Crystallographica. Section D, Biological Crystallography. 58: 2173-4. PMID 12454491 DOI: 10.1107/S0907444902016803  0.324
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