Harnessing conformational plasticity to generate designer enzymes
Recent years have witnessed an explosion of interest in understanding the role of
conformational dynamics both in the evolution of new enzymatic activities from existing …
conformational dynamics both in the evolution of new enzymatic activities from existing …
Mechanisms of protein evolution
How do proteins evolve? How do changes in sequence mediate changes in protein
structure, and in turn in function? This question has multiple angles, ranging from …
structure, and in turn in function? This question has multiple angles, ranging from …
ECOD: integrating classifications of protein domains from experimental and predicted structures
The evolutionary classification of protein domains (ECOD) classifies protein domains using
a combination of sequence and structural data (http://prodata. swmed. edu/ecod). Here we …
a combination of sequence and structural data (http://prodata. swmed. edu/ecod). Here we …
Classification of domains in predicted structures of the human proteome
Recent advances in protein structure prediction have generated accurate structures of
previously uncharacterized human proteins. Identifying domains in these predicted …
previously uncharacterized human proteins. Identifying domains in these predicted …
On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment
This article is dedicated to the memory of Michael G. Rossmann. Dating back to the last
universal common ancestor, P-loop NTPases and Rossmanns comprise the most ubiquitous …
universal common ancestor, P-loop NTPases and Rossmanns comprise the most ubiquitous …
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2
Protein structure prediction has now been deployed widely across several different large
protein sets. Large-scale domain annotation of these predictions can aid in the development …
protein sets. Large-scale domain annotation of these predictions can aid in the development …
DPAM: A domain parser for AlphaFold models
The recent breakthroughs in structure prediction, where methods such as AlphaFold
demonstrated near‐atomic accuracy, herald a paradigm shift in structural biology. The 200 …
demonstrated near‐atomic accuracy, herald a paradigm shift in structural biology. The 200 …
[HTML][HTML] Decreased liver B vitamin-related enzymes as a metabolic hallmark of cancer cachexia
Y Kojima, E Mishiro-Sato, T Fujishita, K Satoh… - Nature …, 2023 - nature.com
Cancer cachexia is a complex metabolic disorder accounting for~ 20% of cancer-related
deaths, yet its metabolic landscape remains unexplored. Here, we report a decrease in B …
deaths, yet its metabolic landscape remains unexplored. Here, we report a decrease in B …
Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins
The Rossmann fold enzymes are involved in essential biochemical pathways such as
nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors …
nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors …
Quinolinate Synthase: An Example of the Roles of the Second and Outer Coordination Spheres in Enzyme Catalysis
JC Fontecilla-Camps, A Volbeda - Chemical Reviews, 2022 - ACS Publications
The activation energy barrier of biochemical reactions is normally lowered by an enzyme
catalyst, which directly helps the weakening of the bond (s) to be broken. In many …
catalyst, which directly helps the weakening of the bond (s) to be broken. In many …