Protein design: toward functional metalloenzymes

F Yu, VM Cangelosi, ML Zastrow, M Tegoni… - Chemical …, 2014 - ACS Publications
Protein design is a valuable tool for understanding the fundamental factors that dictate
protein structure and function. The field of protein design has seen significant progress over …

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 …

Scaffolding protein functional sites using deep learning

J Wang, S Lisanza, D Juergens, D Tischer, JL Watson… - Science, 2022 - science.org
The binding and catalytic functions of proteins are generally mediated by a small number of
functional residues held in place by the overall protein structure. Here, we describe deep …

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 …

Rational design of metalloenzymes: From single to multiple active sites

YW Lin - Coordination Chemistry Reviews, 2017 - Elsevier
Artificial metalloenzymes combine the advantages of both natural enzymes and chemically
synthesized models, which have achieved significant progress in the last decade. This …

Computational design of virus-like protein assemblies on carbon nanotube surfaces

G Grigoryan, YH Kim, R Acharya, K Axelrod, RM Jain… - Science, 2011 - science.org
There is a general need for the engineering of protein-like molecules that organize into
geometrically specific superstructures on molecular surfaces, directing further …

Deep learning methods for designing proteins scaffolding functional sites

J Wang, S Lisanza, D Juergens, D Tischer… - BioRxiv, 2021 - biorxiv.org
Current approaches to de novo design of proteins harboring a desired binding or catalytic
motif require pre-specification of an overall fold or secondary structure composition, and …

Designing functional metalloproteins: From structural to catalytic metal sites

ML Zastrow, VL Pecoraro - Coordination chemistry reviews, 2013 - Elsevier
Metalloenzymes efficiently catalyze some of the most important and difficult reactions in
nature. For many years, coordination chemists have effectively used small molecule models …

The effect of oxygenated fuel properties on diesel spray combustion and soot formation

W Park, S Park, RD Reitz, E Kurtz - Combustion and Flame, 2017 - Elsevier
Diesel engines have advantages due to their potential for high fuel conversion efficiency.
However, it is necessary to reduce pollutant emissions, particularly NOx and soot to meet …

Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins

AJ Reig, MM Pires, RA Snyder, Y Wu, H Jo, DW Kulp… - Nature …, 2012 - nature.com
De novo proteins provide a unique opportunity to investigate the structure–function
relationships of metalloproteins in a minimal, well-defined and controlled scaffold. Here, we …