About this Research Topic
This Research Topic is Volume II of a series. The previous volume can be found here: Computational and Experimental Insights in Redox-Coupled Proton Pumping in Proteins
Enzymes that couple catalytic reactions to translocation of ions across membranes are widespread in biology. For instance, proteins involved in key biological processes such as photosynthesis, cell respiration and nitrogen fixation perform proton or ion transfer across the membrane to fulfil the energetic demands of organisms. Understanding such processes is central to the development of novel sustainable energy-generating devices and chemical compounds that can be used to treat diseases caused by protein dysfunction. However, due to difficulties in obtaining dynamical data from structural biology approaches, time-resolved spectroscopy, electrochemical studies and multiscale computations such as molecular dynamics simulations are the methods of choice. Computational approaches when combined with biochemical/biophysical experiments allow us to achieve an unparalleled view at high spatial and temporal resolutions and delve deeply into the mechanism of enzymes. In this Research Topic, we will cover the latest developments in the field of proton and ion translocating bioenergetic systems studied with experimental and/or computational approaches, including new methodological developments and improvements.
Even though reactions involving a single charge particle such as an electron and/or a proton or ion are simple, it is extremely challenging to study these at an atomistic level. This is due to the very large number of degrees of freedom and complexity of surroundings that involve very diverse molecules such as lipids, proteins, water and ions. Central questions include: how is long-ranged charge-charge coupling achieved in bioenergetic enzymes with high thermodynamic and kinetic efficiency? What are those microscopic gates and valves that prevent unwanted reactions to occur? Structural approaches such as cryo EM and time-resolved spectroscopic experiments are the methods of choice to study such aspects, combined with multiscale computer simulations utilizing high-performance supercomputing platforms. Such interdisciplinary approaches are key to understanding the biological energy transduction and its role in human health, as well as bacteria and other bioenergetics systems.
Reviews and Original Research articles are welcome on the topics mentioned below:
• Theory, modeling and experiments of proton-coupled electron transfer (PCET) events, in chemistry and biology
• Modeling and simulations of enzymes catalyzing electron and proton transfer
• Long-ranged proton transfer and role of hydration and conformational dynamics
• Novel multiscale computational approaches
• Novel experimental approaches (incl. high resolution and surface enhanced spectroscopies)
• Bioinformatics and evolutionary aspects of bioenergetic systems
• Application of novel AI/ML-based approaches to bioenergetic systems
• Disease related aspects of bioenergetic systems, including clinically relevant mutations
• Ligand and inhibitor binding to bioenergetic systems, including pathogen specific inhibitors
Enzymes that couple catalytic reactions to translocation of ions across membranes are widespread in biology. For instance, proteins involved in key biological processes such as photosynthesis, cell respiration and nitrogen fixation perform proton or ion transfer across the membrane to fulfil the energetic demands of organisms. Understanding such processes is central to the development of novel sustainable energy-generating devices and chemical compounds that can be used to treat diseases caused by protein dysfunction. However, due to difficulties in obtaining dynamical data from structural biology approaches, time-resolved spectroscopy, electrochemical studies and multiscale computations such as molecular dynamics simulations are the methods of choice. Computational approaches when combined with biochemical/biophysical experiments allow us to achieve an unparalleled view at high spatial and temporal resolutions and delve deeply into the mechanism of enzymes. In this Research Topic, we will cover the latest developments in the field of proton and ion translocating bioenergetic systems studied with experimental and/or computational approaches, including new methodological developments and improvements.
Even though reactions involving a single charge particle such as an electron and/or a proton or ion are simple, it is extremely challenging to study these at an atomistic level. This is due to the very large number of degrees of freedom and complexity of surroundings that involve very diverse molecules such as lipids, proteins, water and ions. Central questions include: how is long-ranged charge-charge coupling achieved in bioenergetic enzymes with high thermodynamic and kinetic efficiency? What are those microscopic gates and valves that prevent unwanted reactions to occur? Structural approaches such as cryo EM and time-resolved spectroscopic experiments are the methods of choice to study such aspects, combined with multiscale computer simulations utilizing high-performance supercomputing platforms. Such interdisciplinary approaches are key to understanding the biological energy transduction and its role in human health, as well as bacteria and other bioenergetics systems.
Reviews and Original Research articles are welcome on the topics mentioned below:
• Theory, modeling and experiments of proton-coupled electron transfer (PCET) events, in chemistry and biology
• Modeling and simulations of enzymes catalyzing electron and proton transfer
• Long-ranged proton transfer and role of hydration and conformational dynamics
• Novel multiscale computational approaches
• Novel experimental approaches (incl. high resolution and surface enhanced spectroscopies)
• Bioinformatics and evolutionary aspects of bioenergetic systems
• Application of novel AI/ML-based approaches to bioenergetic systems
• Disease related aspects of bioenergetic systems, including clinically relevant mutations
• Ligand and inhibitor binding to bioenergetic systems, including pathogen specific inhibitors
Keywords: proton pumping, ion translocation, PCET, multiscale modelling, computer simulations, kinetic experiments, phylogenetics
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
