uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.ORCID iD: 0000-0002-2260-8493
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
Forschungszentrum Jülich, Germany.
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.ORCID iD: 0000-0002-1834-7358
Show others and affiliations
2018 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 140, no 46, p. 15889-15903Article in journal (Refereed) Published
Abstract [en]

Conformational changes are crucial for the catalytic action of many enzymes. A prototypical and well-studied example is loop opening and closure in triosephosphate isomerase (TIM), which is thought to determine the rate of catalytic turnover in many circumstances. Specifically, TIM loop 6 “grips” the phosphodianion of the substrate and, together with a change in loop 7, sets up the TIM active site for efficient catalysis. Crystal structures of TIM typically show an open or a closed conformation of loop 6, with the tip of the loop moving ∼7 Å between conformations. Many studies have interpreted this motion as a two-state, rigid-body transition. Here, we use extensive molecular dynamics simulations, with both conventional and enhanced sampling techniques, to analyze loop motion in apo and substrate-bound TIM in detail, using five crystal structures of the dimeric TIM from Saccharomyces cerevisiae. We find that loop 6 is highly flexible and samples multiple conformational states. Empirical valence bond simulations of the first reaction step show that slight displacements away from the fully closed-loop conformation can be sufficient to abolish most of the catalytic activity; full closure is required for efficient reaction. The conformational change of the loops in TIM is thus not a simple “open and shut” case and is crucial for its catalytic action. Our detailed analysis of loop motion in a highly efficient enzyme highlights the complexity of loop conformational changes and their role in biological catalysis.

Place, publisher, year, edition, pages
2018. Vol. 140, no 46, p. 15889-15903
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:uu:diva-367313DOI: 10.1021/jacs.8b09378ISI: 000451496800048PubMedID: 30362343OAI: oai:DiVA.org:uu-367313DiVA, id: diva2:1266938
Funder
Swedish Research CouncilSwedish National Infrastructure for Computing (SNIC), 2016/1-293Swedish National Infrastructure for Computing (SNIC), 2017/12-11Available from: 2018-11-29 Created: 2018-11-29 Last updated: 2019-12-04Bibliographically approved
In thesis
1. Computational Modeling of the Structure, Function and Dynamics of Biomolecular Systems
Open this publication in new window or tab >>Computational Modeling of the Structure, Function and Dynamics of Biomolecular Systems
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Proteins are a structurally diverse and functionally versatile class of biomolecules. They perform a variety of life-sustaining biological processes with utmost efficiency. A profound understanding of protein function requires knowledge of its structure. Experimentally determined protein structures can serve as a starting point for computer simulations in order to study their dynamic behavior at a molecular level. In this thesis, computational methods have been used to understand structure-function relationships in two classes of proteins - intrinsically disordered proteins (IDP) and enzymes.

Misfolding and subsequent aggregation of the amyloid beta (Aβ) peptide, an IDP, is associated with the progression of Alzheimer’s disease. Besides enriching our understanding of structural dynamics, computational studies on a medically relevant IDP such as Aβ can potentially guide therapeutic development. In the present work, binding interactions of the monomeric form of this peptide with biologically relevant molecular species such as divalent metal ions (Zn2+, Cu2+, Mn2+) and amphiphilic surfactants were characterized using long timescale molecular dynamics (MD) simulations. Among the metal ions, while Zn2+ and Cu2+ maintained coordination to a well-defined binding site in Aβ, Mn2+-binding was observed to be comparatively weak and transient. Surfactants with charged headgroups displayed strong binding interaction with Aβ. Complemented by biophysical experiments, these studies provided a multifaceted perspective of Aβ interactions with the partner molecules.

Triosephosphate isomerase (TIM), a highly evolved and catalytically proficient enzyme, was studied using empirical valence bond (EVB) calculations to obtain deeper insights into the catalytic reaction mechanism. Multiple structural features of TIM such as the flexible loop and preorganized active site residues were investigated for their role in enzyme catalysis. The effect of substrate binding was also studied using truncated substrates. Finally, using enhanced sampling methods, dynamic behavior of the catalytically important loop 6 was characterized. The importance of structural stability and flexibility on protein function was illustrated by the work presented in this thesis, thus furthering our scientific understanding of proteins at a molecular level.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2020. p. 72
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1885
Keywords
Molecular Dynamics, Empirical Valence Bond, Enzyme Catalysis, Amyloid Beta, Aβ, Triosephosphate Isomerase, TIM, Computational Biochemistry, Computational Enzymology
National Category
Biochemistry and Molecular Biology Theoretical Chemistry
Research subject
Biochemistry
Identifiers
urn:nbn:se:uu:diva-398169 (URN)978-91-513-0828-9 (ISBN)
Public defence
2020-02-05, B21, BMC, Husargatan 3, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2020-01-14 Created: 2019-12-04 Last updated: 2020-01-14

Open Access in DiVA

fulltext(6214 kB)78 downloads
File information
File name FULLTEXT01.pdfFile size 6214 kBChecksum SHA-512
c12a902bd38ca03f366e8727e9d8a6d2dbef56c5f69a1df12bc90baf1c0c7ef6857643ee5adbbc9f7277e9a9a15ae7f1ff13b2edce1a567115ab87b3d9c3030a
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Authority records BETA

Liao, QinghuaKulkarni, YashrajPetrovic, DusanKamerlin, Shina C. Lynn

Search in DiVA

By author/editor
Liao, QinghuaKulkarni, YashrajPetrovic, DusanKamerlin, Shina C. Lynn
By organisation
Biochemistry
In the same journal
Journal of the American Chemical Society
Biochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 78 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 62 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf