A protein's sequence determines its conformational energy landscape. This, in turn, determines the protein's function. Understanding the evolution of new protein functions therefore requires understanding how mutations alter the protein energy landscape. Ancestral sequence reconstruction (ASR) has proven a valuable tool for tackling this problem. In ASR, one phylogenetically infers the sequences of ancient proteins, allowing characterization of their properties. When coupled to biophysical, biochemical, and functional characterization, ASR can reveal how historical mutations altered the energy landscape of ancient proteins, allowing the evolution of enzyme activity, altered conformations, binding specificity, oligomerization, and many other protein features. In this article, we review how ASR studies have been used to dissect the evolution of energy landscapes. We also discuss ASR studies that reveal how energy landscapes have shaped protein evolution. Finally, we propose that thinking about evolution from the perspective of an energy landscape can improve how we approach and interpret ASR studies.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11192866 | PMC |
http://dx.doi.org/10.1146/annurev-biophys-030722-125440 | DOI Listing |
J Plant Physiol
December 2024
College of Landscape Architecture and Art, Henan Agricultural University, 450002, Zhengzhou, China. Electronic address:
Sucrose is an essential energy substance for tree peony (Paeonia Suffruticosa) floral organ development. However, little is known about the sucrose regulatory network in tree peony. In this study, the promoter sequence of the tree peony sucrose transporter gene PsSUT2 was cloned.
View Article and Find Full Text PDFCarbohydr Res
December 2024
Department of Physics, Rayat Shikshan Sanstha's Dada Patil Mahavidyalaya, Karjat, Dist - Ahemadnagar, M.S. 414 402, India.
The discovery of branched molecules like dextrin by Schardinger in 1903 marked the inception of cyclodextrin (CD) utilization, catalyzing its journey from laboratory experimentation to widespread commercialization within the pharmaceutical industry. CD, a cyclic oligosaccharide containing glucopyranose units, acts as a versatile guest molecule, forming inclusion complexes (ICs) with various host molecules. Computational studies have become instrumental in elucidating the intricate interactions between β-CD and guest molecules, enabling the prediction of binding energy, forces, affinity, and complex stability.
View Article and Find Full Text PDFEnviron Monit Assess
December 2024
Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.
Soil conditions of croplands are a frequent topic of scientific research. In contrast, less is known about large-scale commercial plantations of perennial crops such as oil palm. Oil palm is a globally important tropical commodity crop which contributes to both food and energy security due to its exceptional productivity.
View Article and Find Full Text PDFInt J Biol Macromol
December 2024
Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, MS (Maharashtra), India. Electronic address:
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health challenge due to the emergence of drug-resistant strains. This study targets Flavin-dependent thymidylate synthase (ThyX), an essential enzyme in the thymidylate biosynthesis pathway crucial for bacterial DNA replication. We utilized advanced computational techniques, including molecular dynamics (MD) simulations and interaction energy analysis, to examine the binding interactions and stability of various thiazole-thiadiazole compounds with Mtb ThyX.
View Article and Find Full Text PDFNano Lett
December 2024
Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany.
Charge-density waves (CDWs) are correlated states of matter, in which the electronic density is modulated periodically due to electronic and phononic interactions. Often, CDW phases coexist with other correlated states, such as superconductivity, spin-density waves, or Mott insulators. Controlling CDW phases may, therefore, enable the manipulation of the energy landscape of these interacting states.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!