Peptides before and during the nucleotide world: An origins story emphasizing cooperation between proteins and nucleic acids

SD Fried, K Fujishima, M Makarov… - Journal of the …, 2022 - royalsocietypublishing.org
Recent developments in Origins of Life research have focused on substantiating the
narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular …

Peptides en route from prebiotic to biotic catalysis

K Hlouchová - Accounts of Chemical Research, 2024 - ACS Publications
Conspectus In the quest to understand prebiotic catalysis, different molecular entities, mainly
minerals, metal ions, organic cofactors, and ribozymes, have been implied as key players. Of …

Accelerating cryptic pocket discovery using AlphaFold

A Meller, S Bhakat, S Solieva… - Journal of chemical …, 2023 - ACS Publications
Cryptic pockets, or pockets absent in ligand-free, experimentally determined structures, hold
great potential as drug targets. However, cryptic pocket openings are often beyond the reach …

Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains

A Meller, JM Lotthammer, LG Smith, B Novak, LA Lee… - Elife, 2023 - elifesciences.org
The design of compounds that can discriminate between closely related target proteins
remains a central challenge in drug discovery. Specific therapeutics targeting the highly …

Allosteric regulation of the 20S proteasome by the Catalytic Core Regulators (CCRs) family

FK Deshmukh, G Ben-Nissan, MA Olshina… - Nature …, 2023 - nature.com
Controlled degradation of proteins is necessary for ensuring their abundance and sustaining
a healthy and accurately functioning proteome. One of the degradation routes involves the …

Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer

Y Bromberg, AA Aptekmann, Y Mahlich, L Cook… - Science …, 2022 - science.org
Biological redox reactions drive planetary biogeochemical cycles. Using a novel, structure-
guided sequence analysis of proteins, we explored the patterns of evolution of enzymes …

pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models

K Kaminski, J Ludwiczak, K Pawlicki, V Alva… - …, 2023 - academic.oup.com
Motivation The detection of homology through sequence comparison is a typical first step in
the study of protein function and evolution. In this work, we explore the applicability of …

Bridging themes: short protein segments found in different architectures

R Kolodny, S Nepomnyachiy, DS Tawfik… - … biology and evolution, 2021 - academic.oup.com
The vast majority of theoretically possible polypeptide chains do not fold, let alone confer
function. Hence, protein evolution from preexisting building blocks has clear potential …

Mechanisms of hexameric helicases

AJ Fernandez, JM Berger - Critical reviews in biochemistry and …, 2021 - Taylor & Francis
Ring-shaped hexameric helicases are essential motor proteins that separate duplex nucleic
acid strands for DNA replication, recombination, and transcriptional regulation. Two …

Exploiting enzyme evolution for computational protein design

GP Pinto, M Corbella, AO Demkiv… - Trends in Biochemical …, 2022 - cell.com
Recent years have seen an explosion of interest in understanding the physicochemical
parameters that shape enzyme evolution, as well as substantial advances in computational …