Sandbox Reserved 931

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This Sandbox is Reserved from 01/04/2014, through 30/06/2014 for use in the course "510042. Protein structure, function and folding" taught by Prof Adrian Goldman, Tommi Kajander, Taru Meri, Konstantin Kogan and Juho Kellosalo at the University of Helsinki. This reservation includes Sandbox Reserved 923 through Sandbox Reserved 947.

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Contents 1 LINE-1 ORF1 Protein 2 Introduction 3 Structure 3.1 Stabilization of the Trimeric Structure 4 A Cool Movie

LINE-1 ORF1 Protein

Long interspersed element 1 (LINE1) open reading frame 1 (L1ORF1) is a LINE-type retrotransposon (class I-transposon) in humans that is responsible for retrotransposition - a process increasing the DNA variety and size of the genome. The protein localizes to large L1 ribonucleoprotein particles, stress granules and nucleus (ref).

Introduction

During retrotransposition, the RNA transcript is reversely transcribed to DNA and integrated with the genome in different place than the original gene. The process is catalyzed by retrotransposons, which often integrate reverse transcriptase and endonuclease functions required in the process.

L1ORF1 localizes to ribonuclein particles, stress granules and nucleus. Although the protein has general affinity to nucleic acids, it displays a strong cis preference, what makes it bind primarily encoding RNA transcripts (ref). In a process known as target-primed reverse transcription, L1ORF1 reversely transcribes the mRNA at the point of genomic integration (ref) and assists with the integration with the DNA.

Structure

Main part of the L1ORF1 structure was solved by X-ray crystallography by Khazina et al. (ref) in 2011. The crystallized part of the protein is a 338-residue, 40 kDa chain composed of 3 domains: long N-terminal alpha-helical domain, central RNA-recognition and binding domain (RRM) and a C-terminal domain (CTD) (LINK TO THE MONOMER). The domains are connected with two linker regions responsible for structure flexibility. The overall structure of the protein forms an L-shaped pocket formed by N terminal helix and central region with the flexible C-terminal domain “capping” the binding pocket (link to monomer).

Stabilization of the Trimeric Structure

L1ORF1 forms homotrimers in which the unusually long alpha helix (residues 111-153) (according to work of Januszyk these helices begin with residue25) provides the trimerization axis forming a coiled coil structure (trimer overall cartoon). The very long N-terminal helices are stabilized by three unique structural features:

• coordination of two chloride anions on the hydrophobic interface inside the coiled coil structure (Cl close-up) by three asparagines (Asn142) and three arginines (Arg135), what promotes the trimeric state of the coiled coil;
• externally stabilizing hydrogen bonds between coiled coil helices (close-up)
• hydrophobic interactions within the hydrophobic core of the coiled-coil.

The trimerization is additionally stabilized on the C-terminal side of the molecule by 1 hydrogen bond between each RRM (zoom), while the CTD regions remain more flexible and do not interact with one another, what plays significant role in accommodation of RNA molecule.

A Cool Movie

["http://www.nature.com/nsmb/journal/v18/n9/extref/nsmb.2097-S2.mov"|Click]