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Items: 1 to 50 of 178

1.

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.

Matelska D, Shabalin IG, Jabłońska J, Domagalski MJ, Kutner J, Ginalski K, Minor W.

BMC Evol Biol. 2018 Dec 22;18(1):199. doi: 10.1186/s12862-018-1309-8.

2.

A Gcn5-related N-acetyltransferase (GNAT) capable of acetylating polymyxin B and colistin antibiotics in vitro.

Czub MP, Zhang B, Chiarelli MP, Majorek KA, Joe L, Porebski PJ, Revilla A, Wu W, Becker DP, Minor W, Kuhn ML.

Biochemistry. 2018 Nov 30. doi: 10.1021/acs.biochem.8b00946. [Epub ahead of print]

PMID:
30499668
3.

A close look onto structural models and primary ligands of metallo-β-lactamases.

Raczynska JE, Shabalin IG, Minor W, Wlodawer A, Jaskolski M.

Drug Resist Updat. 2018 Sep;40:1-12. doi: 10.1016/j.drup.2018.08.001. Epub 2018 Aug 25. Review.

PMID:
30466711
4.

Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment.

Shabalin IG, Porebski PJ, Minor W.

Crystallogr Rev. 2018;24(4):236-262. doi: 10.1080/0889311X.2018.1521805. Epub 2018 Sep 21.

PMID:
30416256
5.

Corrigendum to "A transient post-translational modification of active site cysteine alters binding properties of the parkinsonism protein DJ-1" [Biochem. Biophys. Res. Commun. 504 (1) (2018 Sep 26) 328-333].

Mussakhmetov A, Shumilin IA, Nugmanova R, Shabalin IG, Baizhumanov T, Toibazar D, Khassenov B, Minor W, Utepbergenov D.

Biochem Biophys Res Commun. 2018 Nov 2;505(3):747. doi: 10.1016/j.bbrc.2018.09.174. Epub 2018 Oct 5. No abstract available.

PMID:
30293683
6.

A transient post-translational modification of active site cysteine alters binding properties of the parkinsonism protein DJ-1.

Mussakhmetov A, Shumilin IA, Nugmanova R, Shabalin IG, Baizhumanov T, Toibazar D, Khassenov B, Minor W, Utepbergenov D.

Biochem Biophys Res Commun. 2018 Sep 26;504(1):328-333. doi: 10.1016/j.bbrc.2018.08.190. Epub 2018 Sep 4. Erratum in: Biochem Biophys Res Commun. 2018 Nov 2;505(3):747.

PMID:
30190129
7.

Automatic recognition of ligands in electron density by machine learning.

Kowiel M, Brzezinski D, Porebski PJ, Shabalin IG, Jaskolski M, Minor W.

Bioinformatics. 2019 Feb 1;35(3):452-461. doi: 10.1093/bioinformatics/bty626.

PMID:
30016407
8.

Differences in substrate specificity of V. cholerae FabH enzymes suggest new approaches for the development of novel antibiotics and biofuels.

Hou J, Zheng H, Tzou WS, Cooper DR, Chruszcz M, Chordia MD, Kwon K, Grabowski M, Minor W.

FEBS J. 2018 Aug;285(15):2900-2921. doi: 10.1111/febs.14588. Epub 2018 Jun 30.

PMID:
29917313
9.

Characterizing metal-binding sites in proteins with X-ray crystallography.

Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W.

Nat Protoc. 2018 May;13(5):1062-1090. doi: 10.1038/nprot.2018.018. Epub 2018 Apr 19.

10.

Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.

Kutner J, Shabalin IG, Matelska D, Handing KB, Gasiorowska O, Sroka P, Gorna MW, Ginalski K, Wozniak K, Minor W.

Biochemistry. 2018 Feb 13;57(6):963-977. doi: 10.1021/acs.biochem.7b01137. Epub 2018 Jan 26.

PMID:
29309127
11.

On the Structure and Reaction Mechanism of Human Acireductone Dioxygenase.

Miłaczewska A, Kot E, Amaya JA, Makris TM, Zając M, Korecki J, Chumakov A, Trzewik B, Kędracka-Krok S, Minor W, Chruszcz M, Borowski T.

Chemistry. 2018 Apr 6;24(20):5225-5237. doi: 10.1002/chem.201704617. Epub 2018 Jan 11.

PMID:
29193386
12.

Detect, correct, retract: How to manage incorrect structural models.

Wlodawer A, Dauter Z, Porebski PJ, Minor W, Stanfield R, Jaskolski M, Pozharski E, Weichenberger CX, Rupp B.

FEBS J. 2018 Feb;285(3):444-466. doi: 10.1111/febs.14320. Epub 2017 Nov 27. Review.

13.

Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.

Porebski PJ, Sroka P, Zheng H, Cooper DR, Minor W.

Protein Sci. 2018 Jan;27(1):86-94. doi: 10.1002/pro.3272. Epub 2017 Sep 13.

14.

Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N-acetyltransferases.

Reidl C, Majorek KA, Dang J, Tran D, Jew K, Law M, Payne Y, Minor W, Becker DP, Kuhn ML.

FEBS Lett. 2017 Aug;591(15):2348-2361. doi: 10.1002/1873-3468.12753. Epub 2017 Aug 1.

15.

Databases, Repositories, and Other Data Resources in Structural Biology.

Zheng H, Porebski PJ, Grabowski M, Cooper DR, Minor W.

Methods Mol Biol. 2017;1607:643-665. doi: 10.1007/978-1-4939-7000-1_27. Review.

16.

Circulatory zinc transport is controlled by distinct interdomain sites on mammalian albumins.

Handing KB, Shabalin IG, Kassaar O, Khazaipoul S, Blindauer CA, Stewart AJ, Chruszcz M, Minor W.

Chem Sci. 2016 Nov 1;7(11):6635-6648. doi: 10.1039/c6sc02267g. Epub 2016 Aug 15.

17.

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography.

Zheng H, Langner KM, Shields GP, Hou J, Kowiel M, Allen FH, Murshudov G, Minor W.

Acta Crystallogr D Struct Biol. 2017 Apr 1;73(Pt 4):316-325. doi: 10.1107/S2059798317000584. Epub 2017 Mar 31.

18.

Optimization of overexpression of a chaperone protein of steroid C25 dehydrogenase for biochemical and biophysical characterization.

Niedzialkowska E, Mrugała B, Rugor A, Czub MP, Skotnicka A, Cotelesage JJH, George GN, Szaleniec M, Minor W, Lewiński K.

Protein Expr Purif. 2017 Jun;134:47-62. doi: 10.1016/j.pep.2017.03.019. Epub 2017 Mar 23.

19.

CheckMyMetal: a macromolecular metal-binding validation tool.

Zheng H, Cooper DR, Porebski PJ, Shabalin IG, Handing KB, Minor W.

Acta Crystallogr D Struct Biol. 2017 Mar 1;73(Pt 3):223-233. doi: 10.1107/S2059798317001061. Epub 2017 Feb 22.

20.

Sharing Big Data.

Grabowski M, Minor W.

IUCrJ. 2017 Jan 1;4(Pt 1):3-4. doi: 10.1107/S2052252516020364. eCollection 2017 Jan 1.

21.

The young person's guide to the PDB.

Minor W, Dauter Z, Jaskolski M.

Postepy Biochem. 2016;62(3):242-249. Review.

22.

Antigenic Determinants of Der p 1: Specificity and Cross-Reactivity Associated with IgE Antibody Recognition.

Glesner J, Vailes LD, Schlachter C, Mank N, Minor W, Osinski T, Chruszcz M, Chapman MD, Pomés A.

J Immunol. 2017 Feb 1;198(3):1334-1344. doi: 10.4049/jimmunol.1600072. Epub 2016 Dec 30.

23.

A public database of macromolecular diffraction experiments.

Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W.

Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1181-1193. Epub 2016 Oct 28.

24.

Insight into the 3D structure and substrate specificity of previously uncharacterized GNAT superfamily acetyltransferases from pathogenic bacteria.

Majorek KA, Osinski T, Tran DT, Revilla A, Anderson WF, Minor W, Kuhn ML.

Biochim Biophys Acta Proteins Proteom. 2017 Jan;1865(1):55-64. doi: 10.1016/j.bbapap.2016.10.011. Epub 2016 Oct 23.

25.

An Unwilling Partnership With the Great Society Part II: Physicians Discover Malnutrition, Hunger and the Politics of Hunger.

deShazo RD, Smith R, Minor WF, Skipworth LB.

Am J Med Sci. 2016 Jul;352(1):120-7. doi: 10.1016/j.amjms.2016.04.004. Epub 2016 Apr 16.

PMID:
27432045
26.

An Unwilling Partnership With the Great Society Part I: Head Start and the Beginning of Change in the White Medical Community.

deShazo RD, Minor WF, Smith R, Skipworth LB.

Am J Med Sci. 2016 Jul;352(1):109-19. doi: 10.1016/j.amjms.2016.04.003. Epub 2016 Apr 21.

PMID:
27432044
27.

Correcting the record of structural publications requires joint effort of the community and journal editors.

Rupp B, Wlodawer A, Minor W, Helliwell JR, Jaskolski M.

FEBS J. 2016 Dec;283(24):4452-4457. doi: 10.1111/febs.13765. Epub 2016 Jun 10.

28.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J.

Structure. 2016 Apr 5;24(4):502-508. doi: 10.1016/j.str.2016.02.017.

29.

The impact of structural genomics: the first quindecennial.

Grabowski M, Niedzialkowska E, Zimmerman MD, Minor W.

J Struct Funct Genomics. 2016 Mar;17(1):1-16. doi: 10.1007/s10969-016-9201-5. Epub 2016 Mar 2. Review.

30.

Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug binding site.

Handing KB, Shabalin IG, Szlachta K, Majorek KA, Minor W.

Mol Immunol. 2016 Mar;71:143-151. doi: 10.1016/j.molimm.2016.02.003. Epub 2016 Feb 17.

31.

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

Porebski PJ, Cymborowski M, Pasenkiewicz-Gierula M, Minor W.

Acta Crystallogr D Struct Biol. 2016 Feb;72(Pt 2):266-80. doi: 10.1107/S2059798315024730. Epub 2016 Jan 28.

32.

Safeguarding Structural Data Repositories against Bad Apples.

Minor W, Dauter Z, Helliwell JR, Jaskolski M, Wlodawer A.

Structure. 2016 Feb 2;24(2):216-20. doi: 10.1016/j.str.2015.12.010. Review.

33.

Recombinant production of enzymatically active male contraceptive drug target hTSSK2 - Localization of the TSKS domain phosphorylated by TSSK2.

Shetty J, Sinville R, Shumilin IA, Minor W, Zhang J, Hawkinson JE, Georg GI, Flickinger CJ, Herr JC.

Protein Expr Purif. 2016 May;121:88-96. doi: 10.1016/j.pep.2016.01.009. Epub 2016 Jan 14.

34.

Protein purification and crystallization artifacts: The tale usually not told.

Niedzialkowska E, Gasiorowska O, Handing KB, Majorek KA, Porebski PJ, Shabalin IG, Zasadzinska E, Cymborowski M, Minor W.

Protein Sci. 2016 Mar;25(3):720-33. doi: 10.1002/pro.2861. Epub 2016 Jan 26.

35.

Dissecting the Structural Elements for the Activation of β-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae.

Hou J, Zheng H, Chruszcz M, Zimmerman MD, Shumilin IA, Osinski T, Demas M, Grimshaw S, Minor W.

J Bacteriol. 2015 Nov 9;198(3):463-76. doi: 10.1128/JB.00360-15. Print 2016 Feb 1.

36.

Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.

Shabalin I, Dauter Z, Jaskolski M, Minor W, Wlodawer A.

Acta Crystallogr D Biol Crystallogr. 2015 Sep;71(Pt 9):1965-79. doi: 10.1107/S139900471500629X. Epub 2015 Aug 28.

37.

Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form.

Zheng H, Mandal A, Shumilin IA, Chordia MD, Panneerdoss S, Herr JC, Minor W.

Andrology. 2015 Jul;3(4):756-71. doi: 10.1111/andr.12057.

38.

X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W.

Expert Opin Drug Discov. 2015;10(9):975-89. doi: 10.1517/17460441.2015.1061991. Epub 2015 Jul 15. Review.

39.

100 Years later: Celebrating the contributions of x-ray crystallography to allergy and clinical immunology.

Pomés A, Chruszcz M, Gustchina A, Minor W, Mueller GA, Pedersen LC, Wlodawer A, Chapman MD.

J Allergy Clin Immunol. 2015 Jul;136(1):29-37.e10. doi: 10.1016/j.jaci.2015.05.016. Review.

40.

Structural Analysis of Der p 1-Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies.

Osinski T, Pomés A, Majorek KA, Glesner J, Offermann LR, Vailes LD, Chapman MD, Minor W, Chruszcz M.

J Immunol. 2015 Jul 1;195(1):307-16. doi: 10.4049/jimmunol.1402199. Epub 2015 May 29.

41.

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection.

Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W.

Nucleic Acids Res. 2015 Apr 20;43(7):3789-801. doi: 10.1093/nar/gkv225. Epub 2015 Mar 23.

42.

Data to knowledge: how to get meaning from your result.

Berman HM, Gabanyi MJ, Groom CR, Johnson JE, Murshudov GN, Nicholls RA, Reddy V, Schwede T, Zimmerman MD, Westbrook J, Minor W.

IUCrJ. 2015 Jan 1;2(Pt 1):45-58. doi: 10.1107/S2052252514023306. eCollection 2015 Jan 1. Review.

43.

Structural characterization of the putative ABC-type 2 transporter from Thermotoga maritima MSB8.

Filippova EV, Tkaczuk KL, Chruszcz M, Xu X, Savchenko A, Edwards A, Minor W.

J Struct Funct Genomics. 2014 Dec;15(4):215-22. doi: 10.1007/s10969-014-9189-7. Epub 2014 Oct 12.

44.

Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining.

Dauter Z, Wlodawer A, Minor W, Jaskolski M, Rupp B.

IUCrJ. 2014 Apr 14;1(Pt 3):179-93. doi: 10.1107/S2052252514005442. eCollection 2014 May 1.

45.

Double trouble-Buffer selection and His-tag presence may be responsible for nonreproducibility of biomedical experiments.

Majorek KA, Kuhn ML, Chruszcz M, Anderson WF, Minor W.

Protein Sci. 2014 Oct;23(10):1359-68. doi: 10.1002/pro.2520. Epub 2014 Jul 30.

46.

The crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein CAE31940 from proteobacterium Bordetella bronchiseptica RB50, and evolutionary insight into the NMT1/THI5 family.

Bajor J, Tkaczuk KL, Chruszcz M, Chapman H, Kagan O, Savchenko A, Minor W.

J Struct Funct Genomics. 2014 Jun;15(2):73-81. doi: 10.1007/s10969-014-9180-3. Epub 2014 Jun 8.

47.

The major cockroach allergen Bla g 4 binds tyramine and octopamine.

Offermann LR, Chan SL, Osinski T, Tan YW, Chew FT, Sivaraman J, Mok YK, Minor W, Chruszcz M.

Mol Immunol. 2014 Jul;60(1):86-94. doi: 10.1016/j.molimm.2014.03.016. Epub 2014 Apr 24.

48.

Data management in the modern structural biology and biomedical research environment.

Zimmerman MD, Grabowski M, Domagalski MJ, Maclean EM, Chruszcz M, Minor W.

Methods Mol Biol. 2014;1140:1-25. doi: 10.1007/978-1-4939-0354-2_1.

49.

Factors correlating with significant differences between X-ray structures of myoglobin.

Rashin AA, Domagalski MJ, Zimmermann MT, Minor W, Chruszcz M, Jernigan RL.

Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):481-91. doi: 10.1107/S1399004713028812. Epub 2014 Jan 29.

50.

Edc3 function in yeast and mammals is modulated by interaction with NAD-related compounds.

Walters RW, Shumilin IA, Yoon JH, Minor W, Parker R.

G3 (Bethesda). 2014 Apr 16;4(4):613-22. doi: 10.1534/g3.114.010470.

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