X-ray crystallographic validation of structure predictions used in computational design for protein stabilization

Proteins
Robert J FloorDick B Janssen

Abstract

Protein engineering aimed at enhancing enzyme stability is increasingly supported by computational methods for calculation of mutant folding energies and for the design of disulfide bonds. To examine the accuracy of mutant structure predictions underlying these computational methods, crystal structures of thermostable limonene epoxide hydrolase variants obtained by computational library design were determined. Four different predicted effects indeed contributed to the obtained stabilization: (i) enhanced interactions between a flexible loop close to the N-terminus and the rest of the protein; (ii) improved interactions at the dimer interface; (iii) removal of unsatisfied hydrogen bonding groups; and (iv) introduction of additional positively charged groups at the surface. The structures of an eightfold and an elevenfold mutant showed that most mutations introduced the intended stabilizing interactions, and side-chain conformations were correctly predicted for 72-88% of the point mutations. However, mutations that introduced a disulfide bond in a flexible region had a larger influence on the backbone conformation than predicted. The enzyme active sites were unaltered, in agreement with the observed preservation of catalytic acti...Continue Reading

References

Aug 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·H LiangT C Terwilliger
Oct 8, 1998·Acta Crystallographica. Section D, Biological Crystallography·D WilcockM Coll
Oct 27, 1999·Proceedings of the National Academy of Sciences of the United States of America·B SpillerR C Stevens
Dec 2, 1999·Experimental Cell Research·C V DangK Zeller
Oct 25, 2000·Protein Science : a Publication of the Protein Society·P R PokkuluriM Schiffer
Jan 11, 2001·Biochimica Et Biophysica Acta·M LehmannM Wyss
Apr 17, 2001·Chemical Research in Toxicology·C MorisseauB D Hammock
Jun 19, 2002·Accounts of Chemical Research·Valerie Daggett
Jun 25, 2002·Journal of Molecular Biology·Raphael GueroisLuis Serrano
Sep 24, 2004·Journal of Biotechnology·Vincent G H EijsinkGert Vriend
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·Alexei A VaginGarib N Murshudov
Apr 26, 2005·Biotechnology Advances·W F LiP Lu
Jun 7, 2005·Protein Science : a Publication of the Protein Society·Patrick J Fleming, George D Rose
Dec 22, 2005·Acta Crystallographica. Section D, Biological Crystallography·Philip Evans
Apr 29, 2006·The Journal of Biological Chemistry·Bryan Francis ShawJoan Selverstone Valentine
Aug 8, 2007·Journal of Molecular Biology·Evgeny Krissinel, Kim Henrick
Mar 21, 2008·Nature·Daniela RöthlisbergerDavid Baker
Jul 5, 2008·Journal of Molecular Biology·Shoeb AhmadN Madhusudhana Rao
Aug 9, 2008·Journal of Molecular Biology·Rita MukhopadhyayDomenico Bordo
Feb 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Alexey V GribenkoGeorge I Makhatadze
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Jun 26, 2009·Protein Science : a Publication of the Protein Society·James A Mobley, Anton Poliakov
Oct 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Bettina SchreierBirte Höcker
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Wolfgang Kabsch
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
Oct 16, 2010·Protein Engineering, Design & Selection : PEDS·Helge JochensUwe T Bornscheuer
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Martyn D WinnKeith S Wilson
Sep 10, 2011·Journal of Molecular Biology·Jeffrey W BrownC James McKnight
Feb 7, 2012·Nature Chemical Biology·Sagar D KhareDavid Baker
Mar 20, 2012·Journal of Biotechnology·Janna K BlumAndreas S Bommarius

❮ Previous
Next ❯

Citations

Mar 17, 2017·Journal of Chemical Information and Modeling·Silvia RinaldiGiorgio Colombo
Dec 22, 2016·Protein Engineering, Design & Selection : PEDS·Hesam ArabnejadDick B Janssen
Jan 22, 2020·Chembiochem : a European Journal of Chemical Biology·Hesam ArabnejadDick B Janssen
Mar 17, 2020·Chembiochem : a European Journal of Chemical Biology·Ivan BassaniniSergio Riva
Oct 24, 2020·Chembiochem : a European Journal of Chemical Biology·Guangyue LiManfred T Reetz

❮ Previous
Next ❯

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.

Related Papers

Protein Engineering, Design & Selection : PEDS
Hein J WijmaDick B Janssen
Biochemical and Biophysical Research Communications
G Nemethy, Harold A Scheraga
© 2022 Meta ULC. All rights reserved