Protein folding and tRNA biology
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REVIEW
Protein folding and tRNA biology Mónica Marín 1
&
Tamara Fernández-Calero 1,2 & Ricardo Ehrlich 1,3
Received: 24 July 2017 / Accepted: 28 August 2017 # International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany 2017
Abstract Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this This article is part of a Special Issue on ‘Latin America’ edited by Pietro Ciancaglini and Rosangela Itri. * Mónica Marín [email protected] Tamara Fernández-Calero [email protected] Ricardo Ehrlich [email protected] 1
Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
2
Bioinformatics Unit, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
3
Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations. Keywords In vivo protein folding . Translation kinetics . Codon usage . Codon usage bias . tRNA . tRNA population . tRNA population adaptation . Translation machinery . tRNA quantification . tRNA sequencing . tRNA modified bases
Introduction The research on native and denatured states of proteins has almost a century of history. It seems interesting to begin this review by quoting Hsien Wu’s work on protein denaturation (Wu 1931; Edsall 1995), just prior to the fundamental communication of Mirsky and Pauling (1936). Wu defined denaturation as Ba change in the natural protein molecule whereby it becomes insoluble in solvents in which it was previously soluble.^ Later, when the structure of proteins was yet unknown, he noted: Bwhatever may be the constitution of the protein molecule, its configuration (today we would say conformation) is not completely defined by its structural formula even if this be known.^ And Wu concluded: BEvidence is adduced in support of the hypothesis that the molecule of natural, soluble protein is not a flexible open chain of polypeptid
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