Novel protein folds and their nonsequential structural analogs

Guerler, Aysam; Knapp, Ernst‐Walter

doi:10.1110/ps.035469.108

Cited by 62 publications

(71 citation statements)

References 59 publications

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“…The 3D structures of proteins were aligned using GANGSTA? (Guerler and Knapp 2008) against version 1.75 of the ASTRAL40 compendium. The software uses a nonsequential structural alignment method with proper assignment of helices and strands in the structure.…”

Section: Structural Analysismentioning

confidence: 99%

The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis

2012

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The complexity of modern biochemistry developed gradually on early Earth as new molecules and structures populated the emerging cellular systems. Here, we generate a historical account of the gradual discovery of primordial proteins, cofactors, and molecular functions using phylogenomic information in the sequence of 420 genomes. We focus on structural and functional annotations of the 54 most ancient protein domains. We show how primordial functions are linked to folded structures and how their interaction with cofactors expanded the functional repertoire. We also reveal protocell membranes played a crucial role in early protein evolution and show translation started with RNA and thioester cofactor-mediated aminoacylation. Our findings allow elaboration of an evolutionary model of early biochemistry that is firmly grounded in phylogenomic information and biochemical, biophysical, and structural knowledge. The model describes how primordial α-helical bundles stabilized membranes, how these were decorated by layered arrangements of β-sheets and α-helices, and how these arrangements became globular. Ancient forms of aminoacyl-tRNA synthetase (aaRS) catalytic domains and ancient non-ribosomal protein synthetase (NRPS) modules gave rise to primordial protein synthesis and the ability to generate a code for specificity in their active sites. These structures diversified producing cofactor-binding molecular switches and barrel structures. Accretion of domains and molecules gave rise to modern aaRSs, NRPS, and ribosomal ensembles, first organized around novel emerging cofactors (tRNA and carrier proteins) and then more complex cofactor structures (rRNA). The model explains how the generation of protein structures acted as scaffold for nucleic acids and resulted in crystallization of modern translation.

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Section: Structural Analysismentioning

confidence: 99%

The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis

2012

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“…The scoring used is SAS. [4] MatAlign is a method that uses a distance matrix representation for structure comparison. The algorithm consists of two steps: First, represent the 3D protein structures as 2D distance matrices, then, align these matrices by means of dynamic programming for finding the initial aligned residues pair.…”

Section: A Contact Map Based Methodsmentioning

confidence: 99%

“…These cases in particular can be further revised by applying MUSTANG. [4] consisted of two tests. The first used ASTRAL40 datasets that possess significant structural similarities and compared with TM-Align.…”

Section: Mustang Experimentsmentioning

confidence: 99%

“…The main conclusion drawn by the authors [4] is the claim that, by comparing similarities unsequentially and in reverse order it is possible to find functions and similarities of new folds which there is no current knowledge yet. In addition, nonsequential structure alignment tools can produce additional insight to understand protein structures and fold characteristics.…”

Section: Gangsta + Experimentsmentioning

confidence: 99%

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Evaluation of Novel Protein Structure Comparison Algorithms Based on Objective Function Rankings

Hasegawa

2009

2009 2nd International Conference on Biomedical Engineering and Informatics

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Protein structure comparison is a important and developing area in Bioinformatics. Understanding the protein structure is very useful, since protein structure suffers less evolutionary changes compared to the amino acid sequences. Thus, comparing protein structures provides additional evolution information.However, structure comparison is not straightforward and multiple algorithms for comparison have emerged recently. In this paper we evaluate the performance of algorithms based on contact maps and Cα, and their respective objective function, which is a measure of biological and evolutionary importance. The contributions are a state-of-the-art review of protein structure comparison algorithms that have not been compared with other servers. Further, we compare findings and evaluate them across others methods already proven effective.

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“…The first one, FAST [16] builds alignment between two protein structures by a directionality-based scoring scheme to compare intra-molecular residue-residue distances in two structures. GANGSTA+ [17] performs sequential and nonsequential alignments while assigning the type of secondary structure by focusing only on helices and strands.…”

Section: Consensus: Protein Classification Using the Decision Of Multmentioning

confidence: 99%

Consensus Decision for Protein Structure Classification

Boujenfa¹,

Limam²

2012

JILSA

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The fundamental aim of protein classification is to recognize the family of a given protein and determine its biological function. In the literature, the most common approaches are based on sequence or structure similarity comparisons. Other methods use evolutionary distances between proteins. In order to increase classification performance, this work proposes a novel method, namely Consensus, which combines the decisions of several sequence and structure comparison tools to classify a given structure. Additionally, Consensus uses the evolutionary information of the compared structures. Our method is tested on three databases and evaluated based on different criteria. Performance evaluation of our method shows that it outperforms the different classifiers used separately and gives higher classification performance than a free-alignment method, namely ProtClass.

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Novel protein folds and their nonsequential structural analogs

Cited by 62 publications

References 59 publications

The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis

The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis

Evaluation of Novel Protein Structure Comparison Algorithms Based on Objective Function Rankings

Consensus Decision for Protein Structure Classification

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