Combining free energy calculations with tailored enzyme activity assays to elucidate substrate binding of a phospho-lysine phosphatase.

Chemical Science
Anett HauserChristian P R Hackenberger

Abstract

Studying enzymes that are involved in the regulation of dynamic post-translational modifications (PTMs) is of key importance in proteomics research. Such investigations can be particularly challenging when the modification itself is intrinsically labile. In this article, we elucidate the enzymatic activity of Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase (LHPP) towards different O- and N-phosphorylated peptides by a combined experimental and computational approach. LHPP has been previously described to hydrolyze the phosphoramidate bonds in different small molecule substrates, including phosphorylated lysine (pLys). Taking the instability of the phosphoramidate bond into account, we conducted a carefully adjusted enzymatic assay with various pLys pentapeptides to confirm enzymatic phosphatase activity with LHPP. Molecular docking was employed to explore possible binding poses of the substrates in complex with the enzyme. Molecular dynamics based free energy calculations, which are unique in their accuracy and solid theoretical basis, were further applied to predict relative binding affinity of different substrates. Comparison of simulations with experiments clearly suggested a distinct binding motif of pLys...Continue Reading

References

Nov 1, 1977·Biochemistry·C C ChenR A Smith
Jun 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·M R Webb
Nov 9, 1973·Nature·D L SmtihR A Smith
May 1, 1997·Archives of Biochemistry and Biophysics·H HiraishiA Kumon
Oct 9, 2002·Trends in Biochemical Sciences·Gerard ManningSucha Sudarsanam
Mar 19, 2004·Journal of Medicinal Chemistry·Richard A FriesnerPeter S Shenkin
Mar 19, 2004·Journal of Medicinal Chemistry·Thomas A HalgrenJay L Banks
Jan 25, 2006·Biochemical and Biophysical Research Communications·Eisuke KoikeHajime Sugihara
Jun 23, 2007·Nature Reviews. Molecular Cell Biology·Jeffrey A Ubersax, James E Ferrell
Jun 6, 2009·Annual Review of Biochemistry·Mary Katherine Tarrant, Philip A Cole
May 21, 2010·Biophysical Journal·Daniel Seeliger, Bert L de Groot
Feb 26, 2011·Current Opinion in Structural Biology·John D ChoderaVijay S Pande
Aug 20, 2011·Chemical Communications : Chem Comm·Frank T HofmannFlorian P Seebeck
Aug 15, 2014·Angewandte Chemie·Servaas MichielssensBert L de Groot
Sep 10, 2014·Journal of the American Chemical Society·Jordi Bertran-VicenteChristian P R Hackenberger
Oct 22, 2014·Methods in Molecular Biology·Vytautas GapsysHadas Leonov
Dec 10, 2014·Journal of Computational Chemistry·Vytautas GapsysBert L de Groot
May 29, 2015·Organic & Biomolecular Chemistry·Jordi Bertran-VicenteChristian P R Hackenberger
Oct 27, 2015·Trends in Endocrinology and Metabolism : TEM·Sean J HumphreyMatthias Mann
Mar 1, 2008·Journal of Chemical Theory and Computation·Berk HessErik Lindahl
Jan 16, 2016·Current Drug Discovery Technologies·Brad A Haubrich, David C Swinney
Sep 3, 2016·Nature Communications·Jordi Bertran-VicenteChristian P R Hackenberger
Oct 5, 2016·ACS Chemical Biology·Sara FahsMaja Köhn
Jul 27, 2017·Journal of Medicinal Chemistry·Billy J Williams-NoonanDavid K Chalmers
Mar 22, 2018·Nature·Sravanth K HindupurMichael N Hall
Jun 27, 2018·Biochemical and Biophysical Research Communications·Jiangli ZhengLizhou Sun
Jul 22, 2018·Biochimica Et Biophysica Acta. Molecular Cell Research·Antje Gohla
Oct 10, 2018·Methods in Molecular Biology·Matteo AldeghiVytautas Gapsys
Jan 5, 2019·Chembiochem : a European Journal of Chemical Biology·Kwan Ho JungXin Zhang
Jan 17, 2019·ACS Central Science·Matteo AldeghiBert L de Groot
Mar 27, 2019·ACS Sensors·Yigun ChoiJung-Min Kee
Apr 10, 2019·Nature Chemical Biology·Marcin J SuskiewiczTim Clausen
May 22, 2019·Journal of the American Society for Mass Spectrometry·Martin PenkertEberhard Krause

❮ Previous
Next ❯

Methods Mentioned

BETA
phosphatase assay
Assay
enzymatic assay
X-ray

Software Mentioned

Schrödinger
pmx
GROMACS

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.