De novo protein design, a retrospective

IV Korendovych, WF DeGrado - Quarterly reviews of biophysics, 2020 - cambridge.org
Proteins are molecular machines whose function depends on their ability to achieve
complex folds with precisely defined structural and dynamic properties. The rational design …

De novo metalloprotein design

MJ Chalkley, SI Mann, WF DeGrado - Nature Reviews Chemistry, 2022 - nature.com
Natural metalloproteins perform many functions—ranging from sensing to electron transfer
and catalysis—in which the position and property of each ligand and metal are dictated by …

Catalysis and Electron Transfer in De Novo Designed Metalloproteins

KJ Koebke, TBJ Pinter, WC Pitts, VL Pecoraro - Chemical reviews, 2022 - ACS Publications
One of the hallmark advances in our understanding of metalloprotein function is showcased
in our ability to design new, non-native, catalytically active protein scaffolds. This review …

Geometric and electronic structure/function correlations in non-heme iron enzymes

EI Solomon, TC Brunold, MI Davis, JN Kemsley… - Chemical …, 2000 - ACS Publications
In recent years, significant progress has been made in understanding the geometric and
electronic structures of the active sites of non-heme iron enzymes and the contributions of …

Salt bridges: Geometrically specific, designable interactions

JE Donald, DW Kulp… - … : Structure, Function, and …, 2011 - Wiley Online Library
Salt bridges occur frequently in proteins, providing conformational specificity and
contributing to molecular recognition and catalysis. We present a comprehensive analysis of …

De novo design of a transmembrane Zn2+-transporting four-helix bundle

NH Joh, T Wang, MP Bhate, R Acharya, Y Wu, M Grabe… - Science, 2014 - science.org
The design of functional membrane proteins from first principles represents a grand
challenge in chemistry and structural biology. Here, we report the design of a membrane …

Synthetic models for non-heme carboxylate-bridged diiron metalloproteins: strategies and tactics

EY Tshuva, SJ Lippard - Chemical reviews, 2004 - ACS Publications
Metalloproteins perform a variety of functions in biological systems. The catalysis of several
remarkable chemical transformations occurs at metal centers embedded in the active sites of …

De novo design of four-helix bundle metalloproteins: One scaffold, diverse reactivities

A Lombardi, F Pirro, O Maglio, M Chino… - Accounts of chemical …, 2019 - ACS Publications
Conspectus De novo protein design represents an attractive approach for testing and
extending our understanding of metalloprotein structure and function. Here, we describe our …

Probing designability via a generalized model of helical bundle geometry

G Grigoryan, WF DeGrado - Journal of molecular biology, 2011 - Elsevier
Because the space of folded protein structures is highly degenerate, with recurring
secondary and tertiary motifs, methods for representing protein structure in terms of …

Design and engineering of artificial oxygen-activating metalloenzymes

F Nastri, M Chino, O Maglio… - Chemical Society …, 2016 - pubs.rsc.org
Many efforts are being made in the design and engineering of metalloenzymes with catalytic
properties fulfilling the needs of practical applications. Progress in this field has recently …