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Items: 1 to 50 of 109

1.

CASP13 target classification into tertiary structure prediction categories.

Kinch LN, Kryshtafovych A, Monastyrskyy B, Grishin NV.

Proteins. 2019 Jul 11. doi: 10.1002/prot.25775. [Epub ahead of print]

PMID:
31294862
2.

Assessing predictions on fitness effects of missense variants in calmodulin.

Zhang J, Kinch LN, Cong Q, Katsonis P, Lichtarge O, Savojardo C, Babbi G, Martelli PL, Capriotti E, Casadio R, Garg A, Pal D, Weile J, Sun S, Verby M, Roth FP, Grishin NV.

Hum Mutat. 2019 Sep;40(9):1463-1473. doi: 10.1002/humu.23857. Epub 2019 Sep 3.

PMID:
31283071
3.

ECOD: identification of distant homology among multidomain and transmembrane domain proteins.

Schaeffer RD, Kinch L, Medvedev KE, Pei J, Cheng H, Grishin N.

BMC Mol Cell Biol. 2019 Jun 21;20(1):18. doi: 10.1186/s12860-019-0204-5.

4.

Identification of residues critical for topology inversion of the transmembrane protein TM4SF20 through regulated alternative translocation.

Wang J, Kinch LN, Denard B, Lee CE, Esmaeilzadeh Gharehdaghi E, Grishin N, Ye J.

J Biol Chem. 2019 Apr 12;294(15):6054-6061. doi: 10.1074/jbc.RA119.007681. Epub 2019 Feb 26.

PMID:
30808712
5.

The Legionella effector RavD binds phosphatidylinositol-3-phosphate and helps suppress endolysosomal maturation of the Legionella-containing vacuole.

Pike CM, Boyer-Andersen R, Kinch LN, Caplan JL, Neunuebel MR.

J Biol Chem. 2019 Apr 19;294(16):6405-6415. doi: 10.1074/jbc.RA118.007086. Epub 2019 Feb 7.

PMID:
30733336
6.

Combined Blockade of Activating ERBB2 Mutations and ER Results in Synthetic Lethality of ER+/HER2 Mutant Breast Cancer.

Croessmann S, Formisano L, Kinch LN, Gonzalez-Ericsson PI, Sudhan DR, Nagy RJ, Mathew A, Bernicker EH, Cristofanilli M, He J, Cutler RE Jr, Lalani AS, Miller VA, Lanman RB, Grishin NV, Arteaga CL.

Clin Cancer Res. 2019 Jan 1;25(1):277-289. doi: 10.1158/1078-0432.CCR-18-1544. Epub 2018 Oct 12.

PMID:
30314968
7.

Protein AMPylation by an Evolutionarily Conserved Pseudokinase.

Sreelatha A, Yee SS, Lopez VA, Park BC, Kinch LN, Pilch S, Servage KA, Zhang J, Jiou J, Karasiewicz-Urbańska M, Łobocka M, Grishin NV, Orth K, Kucharczyk R, Pawłowski K, Tomchick DR, Tagliabracci VS.

Cell. 2018 Oct 18;175(3):809-821.e19. doi: 10.1016/j.cell.2018.08.046. Epub 2018 Sep 27.

PMID:
30270044
8.

FlyXCDB-A Resource for Drosophila Cell Surface and Secreted Proteins and Their Extracellular Domains.

Pei J, Kinch LN, Grishin NV.

J Mol Biol. 2018 Sep 14;430(18 Pt B):3353-3411. doi: 10.1016/j.jmb.2018.06.002. Epub 2018 Jun 8.

PMID:
29890119
9.

Functional and evolutionary analysis of viral proteins containing a Rossmann-like fold.

Medvedev KE, Kinch LN, Grishin NV.

Protein Sci. 2018 Aug;27(8):1450-1463. doi: 10.1002/pro.3438. Epub 2018 Jun 13.

10.

Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics.

Abriata LA, Kinch LN, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M.

Proteins. 2018 Mar;86 Suppl 1:16-26. doi: 10.1002/prot.25403. Epub 2017 Oct 24.

PMID:
29044714
11.

Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I.

Zhang J, Kinch LN, Cong Q, Weile J, Sun S, Cote AG, Roth FP, Grishin NV.

Hum Mutat. 2017 Sep;38(9):1051-1063. doi: 10.1002/humu.23293.

12.

Pet10p is a yeast perilipin that stabilizes lipid droplets and promotes their assembly.

Gao Q, Binns DD, Kinch LN, Grishin NV, Ortiz N, Chen X, Goodman JM.

J Cell Biol. 2017 Oct 2;216(10):3199-3217. doi: 10.1083/jcb.201610013. Epub 2017 Aug 11.

13.

Acute Hepatopancreatic Necrosis Disease-Causing Vibrio parahaemolyticus Strains Maintain an Antibacterial Type VI Secretion System with Versatile Effector Repertoires.

Li P, Kinch LN, Ray A, Dalia AB, Cong Q, Nunan LM, Camilli A, Grishin NV, Salomon D, Orth K.

Appl Environ Microbiol. 2017 Jun 16;83(13). pii: e00737-17. doi: 10.1128/AEM.00737-17. Print 2017 Jul 1.

14.

Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins.

Shen J, Cong Q, Kinch LN, Borek D, Otwinowski Z, Grishin NV.

F1000Res. 2016 Nov 3;5:2631. doi: 10.12688/f1000research.9765.1. eCollection 2016.

15.

Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog.

Volkov OA, Kinch L, Ariagno C, Deng X, Zhong S, Grishin N, Tomchick DR, Chen Z, Phillips MA.

Elife. 2016 Dec 15;5. pii: e20198. doi: 10.7554/eLife.20198.

16.

Structure of protein O-mannose kinase reveals a unique active site architecture.

Zhu Q, Venzke D, Walimbe AS, Anderson ME, Fu Q, Kinch LN, Wang W, Chen X, Grishin NV, Huang N, Yu L, Dixon JE, Campbell KP, Xiao J.

Elife. 2016 Nov 23;5. pii: e22238. doi: 10.7554/eLife.22238.

17.

Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei.

Leija C, Rijo-Ferreira F, Kinch LN, Grishin NV, Nischan N, Kohler JJ, Hu Z, Phillips MA.

PLoS Pathog. 2016 Nov 7;12(11):e1006010. doi: 10.1371/journal.ppat.1006010. eCollection 2016 Nov.

18.

Compact Structure Patterns in Proteins.

Chitturi B, Shi S, Kinch LN, Grishin NV.

J Mol Biol. 2016 Oct 23;428(21):4392-4412. doi: 10.1016/j.jmb.2016.07.022. Epub 2016 Aug 4.

PMID:
27498165
19.

Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus.

Ray A, Kinch LN, de Souza Santos M, Grishin NV, Orth K, Salomon D.

MBio. 2016 Jul 26;7(4). pii: e01077-16. doi: 10.1128/mBio.01077-16.

20.

HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing.

Liu H, Liang C, Kollipara RK, Matsui M, Ke X, Jeong BC, Wang Z, Yoo KS, Yadav GP, Kinch LN, Grishin NV, Nam Y, Corey DR, Kittler R, Liu Q.

Mol Cell. 2016 Aug 4;63(3):420-32. doi: 10.1016/j.molcel.2016.06.014. Epub 2016 Jul 14.

21.

Bile salt receptor complex activates a pathogenic type III secretion system.

Li P, Rivera-Cancel G, Kinch LN, Salomon D, Tomchick DR, Grishin NV, Orth K.

Elife. 2016 Jul 5;5. pii: e15718. doi: 10.7554/eLife.15718.

22.

Crystal structure of the human sterol transporter ABCG5/ABCG8.

Lee JY, Kinch LN, Borek DM, Wang J, Wang J, Urbatsch IL, Xie XS, Grishin NV, Cohen JC, Otwinowski Z, Hobbs HH, Rosenbaum DM.

Nature. 2016 May 26;533(7604):561-4. doi: 10.1038/nature17666. Epub 2016 May 4.

23.

Direct Demonstration That Loop1 of Scap Binds to Loop7: A CRUCIAL EVENT IN CHOLESTEROL HOMEOSTASIS.

Zhang Y, Lee KM, Kinch LN, Clark L, Grishin NV, Rosenbaum DM, Brown MS, Goldstein JL, Radhakrishnan A.

J Biol Chem. 2016 Jun 10;291(24):12888-96. doi: 10.1074/jbc.M116.729798. Epub 2016 Apr 11.

24.

Assessment of CASP11 contact-assisted predictions.

Kinch LN, Li W, Monastyrskyy B, Kryshtafovych A, Grishin NV.

Proteins. 2016 Sep;84 Suppl 1:164-80. doi: 10.1002/prot.25020. Epub 2016 Mar 9.

25.

Classification of proteins with shared motifs and internal repeats in the ECOD database.

Schaeffer RD, Kinch LN, Liao Y, Grishin NV.

Protein Sci. 2016 Jul;25(7):1188-203. doi: 10.1002/pro.2893. Epub 2016 Feb 21. Review.

26.

CASP 11 target classification.

Kinch LN, Li W, Schaeffer RD, Dunbrack RL, Monastyrskyy B, Kryshtafovych A, Grishin NV.

Proteins. 2016 Sep;84 Suppl 1:20-33. doi: 10.1002/prot.24982. Epub 2016 Jan 27.

27.

Evaluation of free modeling targets in CASP11 and ROLL.

Kinch LN, Li W, Monastyrskyy B, Kryshtafovych A, Grishin NV.

Proteins. 2016 Sep;84 Suppl 1:51-66. doi: 10.1002/prot.24973. Epub 2016 Jan 20.

28.

Large-scale determination of previously unsolved protein structures using evolutionary information.

Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D.

Elife. 2015 Sep 3;4:e09248. doi: 10.7554/eLife.09248.

29.

Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria.

Salomon D, Klimko JA, Trudgian DC, Kinch LN, Grishin NV, Mirzaei H, Orth K.

PLoS Pathog. 2015 Aug 25;11(8):e1005128. doi: 10.1371/journal.ppat.1005128. eCollection 2015 Aug.

30.

A Single Kinase Generates the Majority of the Secreted Phosphoproteome.

Tagliabracci VS, Wiley SE, Guo X, Kinch LN, Durrant E, Wen J, Xiao J, Cui J, Nguyen KB, Engel JL, Coon JJ, Grishin N, Pinna LA, Pagliarini DJ, Dixon JE.

Cell. 2015 Jun 18;161(7):1619-32. doi: 10.1016/j.cell.2015.05.028.

31.

Deoxyhypusine Modification of Eukaryotic Translation Initiation Factor 5A (eIF5A) Is Essential for Trypanosoma brucei Growth and for Expression of Polyprolyl-containing Proteins.

Nguyen S, Leija C, Kinch L, Regmi S, Li Q, Grishin NV, Phillips MA.

J Biol Chem. 2015 Aug 7;290(32):19987-98. doi: 10.1074/jbc.M115.656785. Epub 2015 Jun 16.

32.

Using homology relations within a database markedly boosts protein sequence similarity search.

Tong J, Sadreyev RI, Pei J, Kinch LN, Grishin NV.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):7003-8. doi: 10.1073/pnas.1424324112. Epub 2015 May 18.

33.

ChSeq: A database of chameleon sequences.

Li W, Kinch LN, Karplus PA, Grishin NV.

Protein Sci. 2015 Jul;24(7):1075-86. doi: 10.1002/pro.2689. Epub 2015 Jun 16. Review.

34.

The secretory pathway kinases.

Sreelatha A, Kinch LN, Tagliabracci VS.

Biochim Biophys Acta. 2015 Oct;1854(10 Pt B):1687-93. doi: 10.1016/j.bbapap.2015.03.015. Epub 2015 Apr 8. Review.

35.

ECOD: an evolutionary classification of protein domains.

Cheng H, Schaeffer RD, Liao Y, Kinch LN, Pei J, Shi S, Kim BH, Grishin NV.

PLoS Comput Biol. 2014 Dec 4;10(12):e1003926. doi: 10.1371/journal.pcbi.1003926. eCollection 2014 Dec.

36.

Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes.

Durinck S, Stawiski EW, Pavía-Jiménez A, Modrusan Z, Kapur P, Jaiswal BS, Zhang N, Toffessi-Tcheuyap V, Nguyen TT, Pahuja KB, Chen YJ, Saleem S, Chaudhuri S, Heldens S, Jackson M, Peña-Llopis S, Guillory J, Toy K, Ha C, Harris CJ, Holloman E, Hill HM, Stinson J, Rivers CS, Janakiraman V, Wang W, Kinch LN, Grishin NV, Haverty PM, Chow B, Gehring JS, Reeder J, Pau G, Wu TD, Margulis V, Lotan Y, Sagalowsky A, Pedrosa I, de Sauvage FJ, Brugarolas J, Seshagiri S.

Nat Genet. 2015 Jan;47(1):13-21. doi: 10.1038/ng.3146. Epub 2014 Nov 17.

37.

Vibrio type III effector VPA1380 is related to the cysteine protease domain of large bacterial toxins.

Calder T, Kinch LN, Fernandez J, Salomon D, Grishin NV, Orth K.

PLoS One. 2014 Aug 6;9(8):e104387. doi: 10.1371/journal.pone.0104387. eCollection 2014.

38.

Conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families.

Pei J, Li W, Kinch LN, Grishin NV.

Protein Sci. 2014 Sep;23(9):1220-34. doi: 10.1002/pro.2503. Epub 2014 Jul 7.

39.

Marker for type VI secretion system effectors.

Salomon D, Kinch LN, Trudgian DC, Guo X, Klimko JA, Grishin NV, Mirzaei H, Orth K.

Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9271-6. doi: 10.1073/pnas.1406110111. Epub 2014 Jun 9.

40.

Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides.

Salomon D, Guo Y, Kinch LN, Grishin NV, Gardner KH, Orth K.

Nat Commun. 2013;4:2973. doi: 10.1038/ncomms3973.

41.

cor, a novel carbon monoxide resistance gene, is essential for Mycobacterium tuberculosis pathogenesis.

Zacharia VM, Manzanillo PS, Nair VR, Marciano DK, Kinch LN, Grishin NV, Cox JS, Shiloh MU.

MBio. 2013 Nov 19;4(6):e00721-13. doi: 10.1128/mBio.00721-13.

42.

EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance.

Wei Y, Zou Z, Becker N, Anderson M, Sumpter R, Xiao G, Kinch L, Koduru P, Christudass CS, Veltri RW, Grishin NV, Peyton M, Minna J, Bhagat G, Levine B.

Cell. 2013 Sep 12;154(6):1269-84. doi: 10.1016/j.cell.2013.08.015.

43.

Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism.

He C, Wei Y, Sun K, Li B, Dong X, Zou Z, Liu Y, Kinch LN, Khan S, Sinha S, Xavier RJ, Grishin NV, Xiao G, Eskelinen EL, Scherer PE, Whistler JL, Levine B.

Cell. 2013 Aug 29;154(5):1085-1099. doi: 10.1016/j.cell.2013.07.035. Epub 2013 Aug 15.

44.

Pclust: protein network visualization highlighting experimental data.

Li W, Kinch LN, Grishin NV.

Bioinformatics. 2013 Oct 15;29(20):2647-8. doi: 10.1093/bioinformatics/btt451. Epub 2013 Aug 5.

45.

Platelet-derived growth factor/vascular endothelial growth factor receptor inactivation by sunitinib results in Tsc1/Tsc2-dependent inhibition of TORC1.

Tran TA, Kinch L, Peña-Llopis S, Kockel L, Grishin N, Jiang H, Brugarolas J.

Mol Cell Biol. 2013 Oct;33(19):3762-79. doi: 10.1128/MCB.01570-12. Epub 2013 Jul 22.

46.

Bioinformatics perspective on rhomboid intramembrane protease evolution and function.

Kinch LN, Grishin NV.

Biochim Biophys Acta. 2013 Dec;1828(12):2937-43. doi: 10.1016/j.bbamem.2013.06.031. Epub 2013 Jul 8. Review.

47.

A novel germline mutation in BAP1 predisposes to familial clear-cell renal cell carcinoma.

Farley MN, Schmidt LS, Mester JL, Pena-Llopis S, Pavia-Jimenez A, Christie A, Vocke CD, Ricketts CJ, Peterson J, Middelton L, Kinch L, Grishin N, Merino MJ, Metwalli AR, Xing C, Xie XJ, Dahia PLM, Eng C, Linehan WM, Brugarolas J.

Mol Cancer Res. 2013 Sep;11(9):1061-1071. doi: 10.1158/1541-7786.MCR-13-0111. Epub 2013 May 24.

48.

Structural basis for Rab1 de-AMPylation by the Legionella pneumophila effector SidD.

Chen Y, Tascón I, Neunuebel MR, Pallara C, Brady J, Kinch LN, Fernández-Recio J, Rojas AL, Machner MP, Hierro A.

PLoS Pathog. 2013;9(5):e1003382. doi: 10.1371/journal.ppat.1003382. Epub 2013 May 16. Erratum in: PLoS Pathog. 2013;9(7). doi:10.1371/annotation/2b8e6418-2496-4ffb-b230-95d90b748086.

49.

Solution structure of the WNK1 autoinhibitory domain, a WNK-specific PF2 domain.

Moon TM, Correa F, Kinch LN, Piala AT, Gardner KH, Goldsmith EJ.

J Mol Biol. 2013 Apr 26;425(8):1245-52. doi: 10.1016/j.jmb.2013.01.031. Epub 2013 Jan 30.

PMID:
23376100
50.

Identification of a candidate therapeutic autophagy-inducing peptide.

Shoji-Kawata S, Sumpter R, Leveno M, Campbell GR, Zou Z, Kinch L, Wilkins AD, Sun Q, Pallauf K, MacDuff D, Huerta C, Virgin HW, Helms JB, Eerland R, Tooze SA, Xavier R, Lenschow DJ, Yamamoto A, King D, Lichtarge O, Grishin NV, Spector SA, Kaloyanova DV, Levine B.

Nature. 2013 Feb 14;494(7436):201-6. doi: 10.1038/nature11866. Epub 2013 Jan 30.

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