Oxygen Activation and Energy Conservation by Cytochrome c Oxidase

M Wikström, K Krab, V Sharma - Chemical reviews, 2018 - ACS Publications
This review focuses on the type A cytochrome c oxidases (C c O), which are found in all
mitochondria and also in several aerobic bacteria. C c O catalyzes the respiratory reduction …

Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019 - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

Biomolecular QM/MM simulations: What are some of the “burning issues”?

Q Cui, T Pal, L **e - The Journal of Physical Chemistry B, 2021 - ACS Publications
QM/MM simulations have become an indispensable tool in many chemical and biochemical
investigations. Considering the tremendous degree of success, including recognition by a …

Resolving chemical dynamics in biological energy conversion: Long-range proton-coupled electron transfer in respiratory complex I

VRI Kaila - Accounts of Chemical Research, 2021 - ACS Publications
Conspectus Biological energy conversion is catalyzed by membrane-bound proteins that
transduce chemical or light energy into energy forms that power endergonic processes in …

Hybrid quantum mechanical/molecular mechanical methods for studying energy transduction in biomolecular machines

T Kubař, M Elstner, Q Cui - Annual review of biophysics, 2023 - annualreviews.org
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become
indispensable tools for the study of biomolecules. In this article, we briefly review the basic …

Transient water wires mediate selective proton transport in designed channel proteins

HT Kratochvil, LC Watkins, M Mravic, JL Thomaston… - Nature …, 2023 - nature.com
Selective proton transport through proteins is essential for forming and using proton
gradients in cells. Protons are conducted along hydrogen-bonded 'wires' of water molecules …

Deactivation blocks proton pathways in the mitochondrial complex I

M Röpke, D Riepl, P Saura, A Di Luca… - Proceedings of the …, 2021 - National Acad Sciences
Cellular respiration is powered by membrane-bound redox enzymes that convert chemical
energy into an electrochemical proton gradient and drive the energy metabolism. By …

Perspective: Quantum mechanical methods in biochemistry and biophysics

Q Cui - The Journal of chemical physics, 2016 - pubs.aip.org
In this perspective article, I discuss several research topics relevant to quantum mechanical
(QM) methods in biophysical and biochemical applications. Due to the immense complexity …

Proton movement and coupling in the POT family of peptide transporters

JL Parker, C Li, A Brinth, Z Wang… - Proceedings of the …, 2017 - National Acad Sciences
POT transporters represent an evolutionarily well-conserved family of proton-coupled
transport systems in biology. An unusual feature of the family is their ability to couple the …

A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces

C Li, GA Voth - Proceedings of the National Academy of …, 2021 - National Acad Sciences
Water-assisted proton transport through confined spaces influences many phenomena in
biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in …