Resolving the fine structure in the energy landscapes of repeat proteins
Year: 2022
Type: article
Abstract: Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein-protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.
Source: QRB Discovery
DOI: 10.1017/qrd.2022.4
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,255
Funders: National Science Foundation, National Aeronautics and Space Administration, Rice University, Fundação de Amparo à Pesquisa do Estado de São Paulo, Consejo Nacional de Investigaciones Científicas y Técnicas, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Nuclear Safety and Security Commission, NASA Astrobiology Institute, Center for Theoretical Biological Physics, Secretaría de Ciencia y Técnica, Universidad de Buenos Aires
Awards: G1200619422, G1590092392, G2062209358, G2314922425, G2431641514, G295657101, G301926269, Studies of energy landscapes of biological macromolecules, G3395635298, G3639665850, G4314141119, G4841891030, G4879814465, Center for Theoretical Biological Physics, G8488581224, G8556403166, LIFE IS ELECTRIC. THE ELECTRONIC CIRCUITRY IS CATALYZED BY A SMALL SUBSET OF PROTEINS THAT FUNCTION AS SOPHISTICATED NANOMACHINES. CURRENTLY VERY LITTLE IS KNOWN ABOUT THE ORIGIN OF PROTEINS ON EARTH AND THEIR EVOLUTION IN EARLY MICROBIAL LIFE. TO FILL THIS KNOWLEDGE GAP THE ENIGMA RESEARCH PROGRAM WILL CARRY OUT EXPERIMENTAL BIOINFORMATIC DATA-DRIVEN ABDUCTIVE STUDIES TO EXPLORE THE ORIGIN OF CATALYSIS THE EVOLUTION OF PROTEIN STRUCTURES IN MICROBIAL ANCESTORS AND THE CO-EVOLUTION OF PROTEINS AND THE GEOSPHERE THROUGH GEOLOGIC TIME. ENIGMA HAS THREE INTEGRATED RESEARCH THEMES FOCUSED ON UNDERSTANDING THE EVOLUTION OF PROTEINS INVOLVED IN ELECTRON TRANSFER AND ENERGY GENERATION. THEME 1 WILL INVESTIGATE THE SYNTHESIS AND FUNCTION OF METALLOPROTEINS IN PREBIOTIC SYSTEMS. EXTANT MICROBIAL PROTEINS WILL BE ANALYZED TO IDENTIFY THE SIMPLEST STRUCTURES THAT CAN PERFORM ELECTRON TRANSFER REACTIONS. USING DE NOVO COMPUTATIONAL PROTEIN DESIGN SMALL PEPTIDES WILL BE SYNTHESIZED AND CHARACTERIZED TO ELUCIDATE THE EARLIEST BIOCHEMICAL REACTIONS IN THE ORIGIN OF LIFE. THEME 2 WILL EXAMINE THE EMERGENT COMPLEXITY OF METALLOPROTEINS IN MICROBIAL ANCESTORS. NEW COMPUTATIONAL METHODS LINKING PROTEIN STRUCTURE AND PHYLOGENY WILL BE DEVELOPED TO STUDY THE EVOLUTION OF METAL BINDING LIGANDS IN PROTEINS. A STRUCTURAL ALIGNMENT-BASED HOMOLOGY APPROACH WILL BE USED TO IDENTIFY THE OLDEST STRUCTURES IN PROTEINS AND TO TRACE THE EARLY EVOLUTION OF METAL BINDING FOLDS. THEME 3 WILL EXPLORE THE CO-EVOLUTION OF PROTEINS AND THE GEOSPHERE. DEEP-TIME DATA ON THE NATURE AND DISTRIBUTION OF REDOX-SENSITIVE ELEMENTS IN ROCKS AND MINERALS WILL BE INTEGRATED WITH PROTEIN STRUCTURAL DATA IN THE PROTEIN DATA BANK. MINERALOGICAL DATA (E.G. MINERAL COMPOSITION SOLUBILITY AND AGE) WILL BE INCORPORATED INTO GEOCHEMICAL MODELS TO CONSTRAIN THE BIOAVAILABILITY OF METALS OVER GEOLOGIC TIME AND METAL BIOAVAILABILITY DURING ARCHEAN AND PROTEROZOIC ERAS WILL USED TO DATE SPECIFIC POSITIONS IN THE EVOLUTIONARY TREE CONSTRUCTED IN THEME 2. THE THREE ENIGMA RESEARCH THEMES ARE DIRECTLY RELEVANT TO THE MAJOR TOPICS SYNTHESIS AND FUNCTION OF MACROMOLECULES IN THE ORIGIN OF LIFE EARLY LIFE AND INCREASING COMPLEXITY AND CO-EVOLUTION OF LIFE AND THE PHYSICAL ENVIRONMENT IDENTIFIED IN THE 2015 ASTROBIOLOGY SCIENCE STRATEGY. FURTHERMORE THE ENIGMA PROGRAM COMPLEMENTS THE NAI CAN 7 TEAMS ON EXPERIMENTAL MICROBIAL GENOMICS (GEORGIA TECH) AND LIFE ON A DYNAMIC EARLY EARTH (UC RIVERSIDE). THE RESULTS OF THE ENIGMA RESEARCH PROGRAM WILL HELP THE NAI ANSWER A CENTRAL QUESTION IN ASTROBIOLOGY: HOW DID PROTEINS EVOLVE TO BECOME THE CATALYSTS OF LIFE ON EARTH?
OpenAlex ID: W4282001771