Work

On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences

Year: 2018

Type: article

Abstract: All known terrestrial proteins are coded as continuous strings of ≈20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method to search for patterns and groupings of patterns in protein sequences using a mathematically precise definition for "repetition", an efficient algorithmic implementation and a robust scoring system with no adjustable parameters. We show that the sequence patterns can be well-separated into disjoint classes according to their recurrence in nested structures. The statistics of the occurrences of patterns indicate that short repetitions are sufficient to account for the differences between natural families and randomized groups of sequences by more than 10 standard deviations, while contiguous sequence patterns shorter than 5 residues are effectively random in their occurrences. A small subset of patterns is sufficient to account for a robust "familiarity" definition between arbitrary sets of sequences.

Source: The Journal of Physical Chemistry B

DOI: 10.1021/acs.jpcb.8b07206

Authors: Pablo Turjanski, Diego U. Ferreiro

Institutions: Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires

Language: English

Topic: Fractal and DNA sequence analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Aeronautics and Space Administration, Consejo Nacional de Investigaciones Científicas y Técnicas, Ministerio de Ciencia, Tecnología e Innovación Productiva, Agencia Nacional de Promoción Científica y Tecnológica

Award: 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?