NDLI: Catalyzed Decomposition of Urea. Molecular Dynamics Simulations of the Binding of Urea to Urease

Content Provider	PubMed Central
Author	Estiu, Guillermina Merz, Kenneth M.
Abstract	We present the results of molecular dynamics simulations on the urea/urease system. The starting structure was prepared from the 2.0Å crystal structure of Benini et al. of DAP-inhibited urease (PDB code 3UBP),1 and the trimeric structure (2479 residues) resulted in 180K atoms after solvation by water. The force field parameters were derived using the bonded model approach described by Hoops et al.2 Three different systems were analyzed, each one modeling a different protonation pattern for the His320 and His219 residues. In each case, the three monomers of urease have been analyzed separately. The time averaged structures observed in the three monomers suggest that urease could follow two different competitive mechanisms. A “protein assisted proton transfer” mechanism points to Asp221 as crucial for catalysis. An “Asp mediated proton transfer” involves the transfer of a proton from the bridging OH to a NH2 moiety of urea, assisted by Asp360 in the active site. The impact of the simulation results on our understanding of urease catalysis are discussed in detail.
Related Links	http://dx.doi.org/10.1021/bi052020p
Ending Page	4443
Page Count	15
Starting Page	4429
File Format	PDF
ISSN	00062960
e-ISSN	15204995
Journal	Biochemistry
Issue Number	14
Volume Number	45
Language	English
Publisher Date	2006-04-01
Access Restriction	Open
Subject Keyword	Biochemistry Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Biochemistry

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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