دورية أكاديمية
أعرض في EDS

Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from Yersinia pseudotuberculosis .

التفاصيل البيبلوغرافية
العنوان: Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from Yersinia pseudotuberculosis .
المؤلفون: Ramírez MB; Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla CP 72570, Mexico., Urzúa LS; Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla CP 72570, Mexico., Martínez MLÁM; Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla CP 72410, Mexico., Morales LJM; Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla CP 72570, Mexico.
المصدر: International journal of molecular sciences [Int J Mol Sci] 2023 Feb 16; Vol. 24 (4). Date of Electronic Publication: 2023 Feb 16.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI, [2000-
مواضيع طبية MeSH: Bacterial Proteins*/metabolism , Molecular Chaperones*/metabolism , Periplasmic Binding Proteins*/metabolism , Yersinia pseudotuberculosis*/metabolism, Animals ; Rabbits ; Binding Sites ; Carrier Proteins/metabolism ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Ligands ; Protein Binding
مستخلص: The function of chaperones is to correct or degrade misfolded proteins inside the cell. Classic molecular chaperones such as GroEL and DnaK have not been found in the periplasm of Yersinia pseudotuberculosis . Some periplasmic substrate-binding proteins could be bifunctional, such as OppA. Using bioinformatic tools, we try to elucidate the nature of the interactions between OppA and ligands from four proteins with different oligomeric states. Using the crystal structure of the proteins Mal12 alpha-glucosidase from Saccharomyces cerevisiae S288C, LDH rabbit muscle lactate dehydrogenase, Eco RI endonuclease from Escherichia coli and THG Geotrichum candidum lipase, a hundred models were obtained in total, including five different ligands from each enzyme with five conformations of each ligand. The best values for Mal12 stem from ligands 4 and 5, with conformation 5 for both; for LDH, ligands 1 and 4, with conformations 2 and 4, respectively; for Eco RI, ligands 3 and 5, with conformation 1 for both; and for THG, ligands 2 and 3, with conformation 1 for both. The interactions were analyzed with LigProt, and the length of the hydrogen bridges has an average of 2.8 to 3.0 Å. The interaction within the OppA pocket is energetically favored due to the formation of hydrogen bonds both of OppA and of the selected enzymes. The Asp 419 residue is important in these junctions.
References: J Bacteriol. 1996 Mar;178(6):1770-3. (PMID: 8626309)
FEMS Microbiol Lett. 1997 Aug 1;153(1):63-9. (PMID: 9252573)
Biochim Biophys Acta. 2014 Aug;1843(8):1517-28. (PMID: 24239929)
Elife. 2019 Mar 22;8:. (PMID: 30900991)
Front Mol Biosci. 2021 Oct 25;8:762005. (PMID: 34760928)
J Mol Biol. 2006 Nov 17;364(1):1-8. (PMID: 17007876)
PLoS One. 2010 Feb 25;5(2):e9383. (PMID: 20195530)
J Bacteriol. 2000 Mar;182(6):1600-8. (PMID: 10692365)
Clin Microbiol Rev. 1997 Jan;10(1):35-66. (PMID: 8993858)
J Pathog. 2011;2011:182051. (PMID: 22567322)
Front Mol Biosci. 2022 Oct 24;9:1026724. (PMID: 36353734)
mBio. 2018 Jan 16;9(1):. (PMID: 29339428)
Arch Microbiol. 2022 Jan 19;204(2):144. (PMID: 35044532)
Protein Sci. 1999 Jul;8(7):1432-44. (PMID: 10422831)
Nature. 2011 Jul 20;475(7356):324-32. (PMID: 21776078)
Acta Crystallogr D Biol Crystallogr. 2007 Nov;63(Pt 11):1185-93. (PMID: 18007034)
Structure. 1995 Dec 15;3(12):1395-406. (PMID: 8747465)
J Biol Chem. 1997 Jun 20;272(25):15607-12. (PMID: 9188448)
J Biol Chem. 2019 Feb 8;294(6):2074-2075. (PMID: 30626733)
Res Microbiol. 2019 Nov - Dec;170(8):374-380. (PMID: 31376483)
J Comput Chem. 2004 Oct;25(13):1605-12. (PMID: 15264254)
Nat Protoc. 2020 May;15(5):1829-1852. (PMID: 32269383)
J Biol Chem. 2004 Jul 30;279(31):32301-7. (PMID: 15169767)
Subcell Biochem. 2019;92:169-186. (PMID: 31214987)
Res Microbiol. 2019 Nov - Dec;170(8):407-416. (PMID: 31279084)
Biochim Biophys Acta. 2004 Nov 11;1694(1-3):121-34. (PMID: 15546662)
Front Microbiol. 2017 Mar 28;8:531. (PMID: 28400767)
EMBO J. 2000 Jul 17;19(14):3649-56. (PMID: 10899119)
Front Mol Biosci. 2021 May 11;8:678697. (PMID: 34046432)
J Mol Biol. 2011 Nov 18;414(1):75-85. (PMID: 21983341)
Mol Cell. 2021 Aug 19;81(16):3294-3309.e12. (PMID: 34293321)
Infect Immun. 2020 Apr 20;88(5):. (PMID: 32094256)
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W310-4. (PMID: 16845016)
J Comput Chem. 2010 Jan 30;31(2):455-61. (PMID: 19499576)
Science. 1994 Jun 10;264(5165):1578-81. (PMID: 8202710)
J Gen Physiol. 2014 Apr;143(4):419-35. (PMID: 24638992)
J Biol Chem. 2021 Nov;297(5):101282. (PMID: 34624315)
Int J Mol Sci. 2019 Jun 10;20(11):. (PMID: 31185645)
J Biol Chem. 2002 Jan 4;277(1):32-9. (PMID: 11602593)
Pflugers Arch. 2020 Sep;472(9):1129-1153. (PMID: 32372286)
Protein Eng. 1995 Feb;8(2):127-34. (PMID: 7630882)
Protein Sci. 1994 Jan;3(1):82-91. (PMID: 8142901)
Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20527-32. (PMID: 24297927)
AMB Express. 2020 Aug 21;10(1):153. (PMID: 32821976)
J Ind Microbiol Biotechnol. 2015 Aug;42(8):1167-74. (PMID: 25998246)
Nat Struct Mol Biol. 2009 Jun;16(6):574-81. (PMID: 19491934)
Biochem J. 2013 Sep 15;454(3):361-9. (PMID: 23988124)
J Bacteriol. 1998 May;180(10):2718-22. (PMID: 9573158)
FEBS J. 2010 Oct;277(20):4205-14. (PMID: 20812985)
FEBS Lett. 2020 Sep;594(17):2770-2781. (PMID: 32446288)
Cell. 2008 Apr 4;133(1):142-53. (PMID: 18394994)
معلومات مُعتمدة: grant number ID Proyecto: 00243 Vicerrectoria de Investigación y Estudios de Posgrado, Benemérita Universidad Autónoma de Puebla
فهرسة مساهمة: Keywords: OppA protein; Yersinia pseudotuberculosis; chaperones; interactions between OppA and ligands
المشرفين على المادة: 0 (Bacterial Proteins)
0 (Carrier Proteins)
0 (Escherichia coli Proteins)
0 (Ligands)
0 (Molecular Chaperones)
0 (Periplasmic Binding Proteins)
0 (oligopeptide-binding protein, bacteria)
تواريخ الأحداث: Date Created: 20230225 Date Completed: 20230327 Latest Revision: 20230327
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC9967938
DOI: 10.3390/ijms24044023
PMID: 36835435
قاعدة البيانات: MEDLINE
الوصف
تدمد:1422-0067
DOI:10.3390/ijms24044023