[HTML][HTML] Gates of enzymes

A Gora, J Brezovsky, J Damborsky - Chemical reviews, 2013 - ACS Publications
Enzymes are very efficient catalysts that are essential for the functioning of living organisms.
The low efficiency of biocatalysts produced de novo relative to those that have evolved …

Substrate tunnels in enzymes: structure–function relationships and computational methodology

LJ Kingsley, MA Lill - Proteins: Structure, Function, and …, 2015 - Wiley Online Library
In enzymes, the active site is the location where incoming substrates are chemically
converted to products. In some enzymes, this site is deeply buried within the core of the …

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures

E Chovancova, A Pavelka, P Benes, O Strnad… - 2012 - journals.plos.org
Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a
large variety of proteins. Characteristics of individual transport pathways, including their …

Neuroglobin: From structure to function in health and disease

P Ascenzi, A di Masi, L Leboffe, M Fiocchetti… - Molecular aspects of …, 2016 - Elsevier
In 2000, the third member of the globin family was discovered in human and mouse brain
and named neuroglobin (Ngb). Ngb is a monomeric 3/3 globin structurally similar to …

CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels

O Vavra, J Filipovic, J Plhak, D Bednar… - …, 2019 - academic.oup.com
Motivation Protein tunnels and channels are key transport pathways that allow ligands to
pass between proteins' external and internal environments. These functionally important …

Software tools for identification, visualization and analysis of protein tunnels and channels

J Brezovsky, E Chovancova, A Gora, A Pavelka… - Biotechnology …, 2013 - Elsevier
Protein structures contain highly complex systems of voids, making up specific features such
as surface clefts or grooves, pockets, protrusions, cavities, pores or channels, and tunnels …

CD95 structure, aggregation and cell signaling

N Levoin, M Jean, P Legembre - Frontiers in Cell and Developmental …, 2020 - frontiersin.org
CD95 is a pre-ligand-associated transmembrane (TM) receptor. The interaction with its
ligand CD95L brings to a next level its aggregation and triggers different signaling …

[PDF][PDF] Engineering of protein tunnels: Keyhole-lock-key model for catalysis by the enzymes with buried active sites

Z Prokop, A Gora, J Brezovsky… - Protein engineering …, 2012 - researchgate.net
Enzymes exhibit a high degree of specificity for the reactions they catalyze and the
substrates involved in these reactions. The eminent specificity of enzymes inspired the …

Influence of the membrane lipophilic environment on the structure and on the substrate access/egress routes of the human aromatase enzyme. A computational study

J Sgrignani, A Magistrato - Journal of chemical information and …, 2012 - ACS Publications
Human aromatase (HA), an enzyme located on the membrane of the endoplasmatic
reticulum, is of crucial biological importance in the biosynthesis of estrogens. High levels of …

Human Mn-superoxide dismutase inactivation by peroxynitrite: a paradigm of metal-catalyzed tyrosine nitration in vitro and in vivo

V Demicheli, DM Moreno, R Radi - Metallomics, 2018 - academic.oup.com
Human MnSOD is a homotetramer and represents an essential mitochondrial antioxidant
enzyme, which catalyzes the dismutation of superoxide radicals (O2˙−) at near diffusion …