Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain

RESEARCH ARTICLE Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain The Quyen Nguyen1,2, Mélanie Chenon1,2, Fernando Vilela1,2, Christophe Velours1,2, Magali Aumont-Nicaise2, Jessica Andreani2, Paloma F. Varela1,2, Paola Llinas1,2*, Julie Ménétrey1,2* 1 Laboratoire d’Enzymologie et Biochimie Structurales (LEBS), CNRS, Université Paris-Sud, 1 avenue de la Terrasse, Gif-sur-Yvette, France, 2 Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France * (PL); (JM) a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Nguyen TQ, Chenon M, Vilela F, Velours C, Aumont-Nicaise M, Andreani J, et al. (2017) Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain. PLoS ONE 12(10): e0186354. https://doi.org/10.1371/ journal.pone.0186354 Editor: Eugene A. Permyakov, Russian Academy of Medical Sciences, RUSSIAN FEDERATION Received: September 5, 2017 Accepted: September 29, 2017 Published: October 16, 2017 Copyright: © 2017 Nguyen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Coordinates and structure factor files have been deposited at the Protein Data Bank under accession numbers 5OJF and 5OJ8 for KLC2-TPR[A1-B6] and KLC1-TPR [A1-B5], respectively. Funding: This work was supported by the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INSB-05, and by grants SFI20121205592 and DOC20160603834 from ARC to J.M and T.Q.N, respectively. Abstract Kinesin1 plays a major role in neuronal transport by recruiting many different cargos through its kinesin light chain (KLC). Various structurally unrelated cargos interact with the conserved tetratricopeptide repeat (TPR) domain of KLC. The N-terminal capping helix of the TPR domain exhibits an atypical sequence and structural features that may contribute to the versatility of the TPR domain to bind different cargos. We determined crystal structures of the TPR domain of both KLC1 and KLC2 encompassing the N-terminal capping helix and show that this helix exhibits two distinct and defined orientations relative to the rest of the TPR domain. Such a difference in orientation gives rise, at the N-terminal part of the groove, to the formation of one hydrophobic pocket, as well as to electrostatic variations at the groove surface. We present a comprehensive structural analysis of available KLC1/2-TPR domain structures that highlights that ligand binding into the groove can be specific of one or the other N-terminal capping helix orientations. Further, structural analysis reveals that the N-terminal capping helix is always involved in crystal packing contacts, especially in a TPR1:TPR1’ contact which highlights its propensity to be a protein–protein interaction site. Together, these results underline that the structural plasticity of the N-terminal capping helix might represent a structural determinant for TPR domain structural versatility in cargo binding. Introduction Kinesins are a superfamily of molecular motor proteins that move along microtubules powered by ATP hydrolysis energy [1]. The active movement of kinesins supports several cellular functions including cell division and transport of cellular cargos [2]. Defects of kinesin functions are involved in various pathologies, including cancer and nervous system, metabolic and cilia diseases [2–4]. Kinesin1 (also known as conventional kinesin or Kif5) plays a major role in neuronal transport by recruiting many different cargos such as organelles, vesicles, mRNA/ proteins complexes and protein assemblies [5,6]. Accumulating evidence suggest a key role for PLOS ONE | https://doi.org/10.1371/journal.pone.0186354 October 16, 2017 1 / 20 Structural plasticity of the N-terminal capping helix of the KLC-TPR domain Competing interests: The authors have declared that no competing interests exist. kinesin1 in several neurological disorders including Alzheimer’s disease [7]. Kinesin1 functions as a hetero-tetramer composed of a dimer of kinesin heavy chains (KHC) bound to two kinesin light chains (KLC) [8]. KHC consists of three regions: a N-terminal globular motor domain (head) that contains the ATP and microtubule binding sites, a central elongated coiled-coil (stalk) responsible for dimerization, and a C-terminal unstructured region (tail) that regulates motor motility and recruits cargos. KLC is also composed of three regions: a Nterminal Heptad Repeat (HR) region that binds to the KHC stalk, a TPR (Tetratrico Peptide Repeat) domain involved in cargo recruitment, and a variable C-terminal region. While only one KLC-like isoform has been found in invertebrates, four KLC isoforms (KLC1-4) have been identified in vertebrates. KLC1/2 isoforms bind several proteins that are associated with axonal transport and neurodegeneration, such as the structurally unrelated JIP1/2 and JIP3/4 (JNK-interacting proteins 1/2 and 3/4) cargos [9–12], as well as the growing family of W-acidic motif (tryptophan residue flanked by acidic residues) cargos including Huntingtin-Associated Protein-1 (HAP1), the type I transmembrane Calsyntenin-1/Alcadein α (CSTN1/Alcα) proteins or the lysosome adaptor SKIP (SifA-Kinesin Interacting Protein) [13–17]. Interestingly, among the different mechanisms that regulate kinesin1 cargo binding, one is KLC auto-inhibition [18]. Within the flexible linker between the HR region and the TPR domain of KLC there is a highly conserved Leucine-Phenylalanine-Proline (LFP) motif flanked by acidic residues that folds back on the TPR domain partly occluding the cargo binding site. However, while auto-inhibition by the LFP motif reduces KLC affinity for WD-motif cargo SKIP, it only marginally reduces affinity for JIP1 [18], suggesting that other mechanisms may regulate cargo binding to the KLC-TPR domain. The basic function of TPR domains is to mediate protein–protein interactions and this can be achieved in a variety of ways [19]. TPR domains are present in a wide range of proteins consisting of several TPR motifs in tandem (from 3 to 16 repeats) [19]. Each motif repeat involves two antiparallel α helices (A and B) which stack together, in a parallel array relative to other motifs, to form an extended molecule with an overall right-handed super-helical architecture. The domain adopts a cradle-shape with helices A of each repeat lining the concave face (or groove) and helices B lining the convex face. A standard “nPR” nomenclature system has been proposed for the TPR family proteins based on variable-length TPR-motifs, where n represents the number of residues in a single repeat [20]. Accordingly, the canonical 34-residue TPR motif is referred to as 34PR motif, (...truncated)