Iterative approach to computational enzyme design.

Proceedings of the National Academy of Sciences of the United States of America
Heidi K PrivettStephen L Mayo

Abstract

A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led...Continue Reading

References

May 1, 1996·Protein Science : a Publication of the Protein Society·B I Dahiyat, S L Mayo
Jun 1, 1997·Protein Science : a Publication of the Protein Society·B I DahiyatS L Mayo
Sep 18, 1997·Proceedings of the National Academy of Sciences of the United States of America·B I Dahiyat, S L Mayo
Jun 23, 1999·Structure·A G Street, S L Mayo
Aug 21, 2001·The Journal of Organic Chemistry·F HollfelderD S Tawfik
Nov 29, 2001·Proceedings of the National Academy of Sciences of the United States of America·D N Bolon, S L Mayo
Dec 20, 2002·Angewandte Chemie·Thomas Steiner
Mar 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Erik W DeblerIan A Wilson
May 11, 2006·Journal of Computational Chemistry·Benjamin D Allen, Stephen L Mayo
Jul 11, 2006·Protein Science : a Publication of the Protein Society·Eric S ZollarsStephen L Mayo
Nov 1, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jonathan Kyle LassilaStephen L Mayo
Mar 8, 2008·Science·Lin JiangDavid Baker
Mar 21, 2008·Nature·Daniela RöthlisbergerDavid Baker
Oct 1, 2009·Journal of the American Chemical Society·Jory Z RuscioTeresa Head-Gordon
Dec 29, 2009·Journal of Molecular Biology·Olga KhersonskyDan S Tawfik
Jul 29, 2010·Protein Science : a Publication of the Protein Society·Gert KissK N Houk
Sep 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Maria P FrushichevaArieh Warshel
Nov 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Roberto A ChicaStephen L Mayo
Feb 1, 2011·Journal of Molecular Biology·Olga KhersonskyDan S Tawfik
Feb 26, 2011·Protein Engineering, Design & Selection : PEDS·Andrew MorinJens Meiler
Apr 13, 2011·Proceedings of the National Academy of Sciences of the United States of America·Ivan V KorendovychWilliam F DeGrado

❮ Previous
Next ❯

Citations

Sep 18, 2012·Journal of Computer-aided Molecular Design·Mats LinderTore Brinck
Nov 26, 1976·Biochimica Et Biophysica Acta·N B TerwilligerE Schabtach
Oct 26, 1977·Biochimica Et Biophysica Acta·R C TerwilligerJ Bonaventura
May 27, 1977·Biochimica Et Biophysica Acta·S N VinogradovH Mizukami
May 29, 1980·Biochimica Et Biophysica Acta·E ChianconeJ Bonaventura
Jul 5, 1986·Journal of Molecular Biology·T Suzuki, T Gotoh
Mar 18, 1982·Biochimica Et Biophysica Acta·M C Chung, H D Ellerton
Mar 22, 1985·Biochimica Et Biophysica Acta·S N VinogradovA V Crewe
Jun 5, 2012·Journal of the American Chemical Society·Alireza ShokriSteven R Kass
Aug 9, 2013·Journal of the American Chemical Society·Antony J BurtonDerek N Woolfson
Jun 12, 2012·Proceedings of the National Academy of Sciences of the United States of America·Olga KhersonskyDan S Tawfik
Jul 22, 2008·BMC Microbiology·Araceli Contreras-RodriguezAhide Lopez-Merino
Oct 12, 2013·PloS One·Matthew J GrisewoodCostas D Maranas
May 13, 2014·PloS One·Kinshuk Raj Srivastava, Susheel Durani
Dec 4, 2012·International Journal of Molecular Sciences·Alexandre BarrozoShina Caroline Lynn Kamerlin
Mar 20, 2014·Nature Communications·Fang ZhengChang-Guo Zhan
Sep 19, 2012·Proceedings of the National Academy of Sciences of the United States of America·Matthew Merski, Brian K Shoichet
Jun 12, 2013·Annual Review of Biochemistry·Donald Hilvert
Jul 21, 2014·Nature Chemical Biology·José Arcadio Farías-RicoBirte Höcker
Aug 2, 2014·Protein Engineering, Design & Selection : PEDS·Bastiaan A van den BergDick de Ridder
Feb 6, 2013·Biochimica Et Biophysica Acta·A LabasM Fuxreiter
Jun 12, 2013·Nature Chemical Biology·Lars GigerDonald Hilvert
Jan 31, 2016·Journal of Molecular Modeling·Jing XueYushan Zhu
Nov 11, 2015·Proceedings of the National Academy of Sciences of the United States of America·Aron BroomElizabeth M Meiering
Dec 23, 2015·The Journal of Physical Chemistry. B·Netaly KhazanovHanoch Senderowitz
Aug 14, 2015·Proceedings of the National Academy of Sciences of the United States of America·Yun MouStephen L Mayo
Jan 9, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jonathan D JouBruce R Donald
Dec 20, 2015·Trends in Biotechnology·Mark J Burk, Stephen Van Dien
Nov 12, 2015·Journal of the American Chemical Society·Yurii S MorozIvan V Korendovych
May 6, 2014·Current Opinion in Biotechnology·Alexandre Zanghellini
Jul 16, 2015·Current Opinion in Chemical Biology·Chiam Yu NgCostas D Maranas
May 8, 2013·Protein Science : a Publication of the Protein Society·Xiaoqiang HuangYushan Zhu
May 8, 2013·The FEBS Journal·Hein J Wijma, Dick B Janssen
Apr 17, 2013·Biotechnology Journal·Ryan J MarcheschiJames C Liao
Mar 13, 2013·EMBO Reports·Ivan Campeotto, Carlos G Acevedo-Rocha
Jul 20, 2012·Protein Science : a Publication of the Protein Society·James A Davey, Roberto A Chica
Dec 18, 2014·Protein Science : a Publication of the Protein Society·Elizabeth A RaymondIvan V Korendovych

❮ 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

Proceedings of the National Academy of Sciences of the United States of America
Olga KhersonskyDan S Tawfik
Protein Science : a Publication of the Protein Society
Gert KissKendall N Houk
Protein Science : a Publication of the Protein Society
Yakov Kipnis, David Baker
Proceedings of the National Academy of Sciences of the United States of America
Maria P FrushichevaArieh Warshel
© 2022 Meta ULC. All rights reserved