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Conformational mobility of active and E-64-inhibited actinidin

Authorized Users Only
2013
Authors
Grozdanović, Milica
Drakulić, Branko
Gavrović-Jankulović, Marija
Article (Published version)
,
Elsevier
Metadata
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Abstract
Background: Actinidin, a protease from kiwifruit, belongs to the C1 family of cysteine proteases. Cysteine proteases were found to be involved in many disease states and are valid therapeutic targets. Actinidin has a wide pH activity range and wide substrate specificity, which makes it a good model system for studying enzyme-substrate interactions. Methods: The influence of inhibitor (E-64) binding on the conformation of actinidin was examined by 2D PAGE, circular dichroism (CD) spectroscopy, hydrophobic ligand binding assay, and molecular dynamics simulations. Results: Significant differences were observed in electrophoretic mobility of proteolytically active and E-64-inhibited actinidin. CD spectrometry and hydrophobic ligand binding assay revealed a difference in conformation between active and inhibited actinidin. Molecular dynamics simulations showed that a loop defined by amino-acid residues 88-104 had greater conformational mobility in the inhibited enzyme than in the active one.... During MD simulations, the covalently bound inhibitor was found to change its conformation from extended to folded, with the guanidino moiety approaching the carboxylate. Conclusions: Conformational mobility of actinidin changes upon binding of the inhibitor, leading to a sequence of events that enables water and ions to protrude into a newly formed cavity of the inhibited enzyme. Drastic conformational mobility of E-64, a common inhibitor of cysteine proteases found in many crystal structures stored in PDB, was also observed. General significance: The analysis of structural changes which occur upon binding of an inhibitor to a cysteine protease provides a valuable starting point for the future design of therapeutic agents. (c) 2013 Elsevier B.V. All rights reserved.

Keywords:
Actinidin / E-64 / Molecular dynamics / Cysteine protease
Source:
Biochimica et Biophysica Acta: General Subjects, 2013, 1830, 10, 4790-4799
Publisher:
  • Elsevier
Funding / projects:
  • Allergens, antibodies, enzymes and small physiologically important molecules: design, structure, function and relevance (RS-172049)
  • Rational design and synthesis of biologically active and coordination compounds and functional materials, relevant for (bio)nanotechnology (RS-172035)
  • Reinforcement of the Faculty of Chemistry, University of Belgrade, towards becoming a Center of Excellence in the region of WB for Molecular Biotechnology and Food research (EU-256716)
  • High-Performance Computing Infrastructure for South East Europe's Research Communities (EU-261499)

DOI: 10.1016/j.bbagen.2013.06.015

ISSN: 0304-4165

PubMed: 23803410

WoS: 000323854900041

Scopus: 2-s2.0-84880183998
[ Google Scholar ]
5
5
URI
https://cer.ihtm.bg.ac.rs/handle/123456789/2714
Collections
  • Radovi istraživača / Researchers' publications
Institution/Community
IHTM
TY  - JOUR
AU  - Grozdanović, Milica
AU  - Drakulić, Branko
AU  - Gavrović-Jankulović, Marija
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2714
AB  - Background: Actinidin, a protease from kiwifruit, belongs to the C1 family of cysteine proteases. Cysteine proteases were found to be involved in many disease states and are valid therapeutic targets. Actinidin has a wide pH activity range and wide substrate specificity, which makes it a good model system for studying enzyme-substrate interactions. Methods: The influence of inhibitor (E-64) binding on the conformation of actinidin was examined by 2D PAGE, circular dichroism (CD) spectroscopy, hydrophobic ligand binding assay, and molecular dynamics simulations. Results: Significant differences were observed in electrophoretic mobility of proteolytically active and E-64-inhibited actinidin. CD spectrometry and hydrophobic ligand binding assay revealed a difference in conformation between active and inhibited actinidin. Molecular dynamics simulations showed that a loop defined by amino-acid residues 88-104 had greater conformational mobility in the inhibited enzyme than in the active one. During MD simulations, the covalently bound inhibitor was found to change its conformation from extended to folded, with the guanidino moiety approaching the carboxylate. Conclusions: Conformational mobility of actinidin changes upon binding of the inhibitor, leading to a sequence of events that enables water and ions to protrude into a newly formed cavity of the inhibited enzyme. Drastic conformational mobility of E-64, a common inhibitor of cysteine proteases found in many crystal structures stored in PDB, was also observed. General significance: The analysis of structural changes which occur upon binding of an inhibitor to a cysteine protease provides a valuable starting point for the future design of therapeutic agents. (c) 2013 Elsevier B.V. All rights reserved.
PB  - Elsevier
T2  - Biochimica et Biophysica Acta: General Subjects
T1  - Conformational mobility of active and E-64-inhibited actinidin
VL  - 1830
IS  - 10
SP  - 4790
EP  - 4799
DO  - 10.1016/j.bbagen.2013.06.015
ER  - 
@article{
author = "Grozdanović, Milica and Drakulić, Branko and Gavrović-Jankulović, Marija",
year = "2013",
abstract = "Background: Actinidin, a protease from kiwifruit, belongs to the C1 family of cysteine proteases. Cysteine proteases were found to be involved in many disease states and are valid therapeutic targets. Actinidin has a wide pH activity range and wide substrate specificity, which makes it a good model system for studying enzyme-substrate interactions. Methods: The influence of inhibitor (E-64) binding on the conformation of actinidin was examined by 2D PAGE, circular dichroism (CD) spectroscopy, hydrophobic ligand binding assay, and molecular dynamics simulations. Results: Significant differences were observed in electrophoretic mobility of proteolytically active and E-64-inhibited actinidin. CD spectrometry and hydrophobic ligand binding assay revealed a difference in conformation between active and inhibited actinidin. Molecular dynamics simulations showed that a loop defined by amino-acid residues 88-104 had greater conformational mobility in the inhibited enzyme than in the active one. During MD simulations, the covalently bound inhibitor was found to change its conformation from extended to folded, with the guanidino moiety approaching the carboxylate. Conclusions: Conformational mobility of actinidin changes upon binding of the inhibitor, leading to a sequence of events that enables water and ions to protrude into a newly formed cavity of the inhibited enzyme. Drastic conformational mobility of E-64, a common inhibitor of cysteine proteases found in many crystal structures stored in PDB, was also observed. General significance: The analysis of structural changes which occur upon binding of an inhibitor to a cysteine protease provides a valuable starting point for the future design of therapeutic agents. (c) 2013 Elsevier B.V. All rights reserved.",
publisher = "Elsevier",
journal = "Biochimica et Biophysica Acta: General Subjects",
title = "Conformational mobility of active and E-64-inhibited actinidin",
volume = "1830",
number = "10",
pages = "4790-4799",
doi = "10.1016/j.bbagen.2013.06.015"
}
Grozdanović, M., Drakulić, B.,& Gavrović-Jankulović, M.. (2013). Conformational mobility of active and E-64-inhibited actinidin. in Biochimica et Biophysica Acta: General Subjects
Elsevier., 1830(10), 4790-4799.
https://doi.org/10.1016/j.bbagen.2013.06.015
Grozdanović M, Drakulić B, Gavrović-Jankulović M. Conformational mobility of active and E-64-inhibited actinidin. in Biochimica et Biophysica Acta: General Subjects. 2013;1830(10):4790-4799.
doi:10.1016/j.bbagen.2013.06.015 .
Grozdanović, Milica, Drakulić, Branko, Gavrović-Jankulović, Marija, "Conformational mobility of active and E-64-inhibited actinidin" in Biochimica et Biophysica Acta: General Subjects, 1830, no. 10 (2013):4790-4799,
https://doi.org/10.1016/j.bbagen.2013.06.015 . .

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