Binding properties of SUMO-interacting motifs (SIMs) in yeastJournal of Molecular Modeling


Christophe Jardin, Anselm H. C. Horn, Heinrich Sticht
Inorganic Chemistry / Organic Chemistry / Physical and Theoretical Chemistry / Computational Theory and Mathematics / Computer Science Applications / Catalysis


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T Sæther, D R Pattabiraman, A H Alm-Kristiansen, L T Vogt-Kielland, T J Gonda, O S Gabrielsen

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Multiparameter Variational Principles

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Binding properties of SUMO-interacting motifs (SIMs) in yeast

Christophe Jardin & Anselm H. C. Horn & Heinrich Sticht

Received: 29 October 2014 /Accepted: 26 January 2015 # Springer-Verlag Berlin Heidelberg 2015

Abstract Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact noncovalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

Keywords Linear motif . Molecular dynamics (MD) simulations . Protein-protein interaction . SUMO-bindingmotif (SBM) . SUMO-interactingmotif (SIM) . SUMO-SIM complexes


Many proteins can achieve their cellular function only when they are part of larger assemblies of two or more proteins. As a matter of fact, protein-protein interactions (PPIs) play a key role in the regulation of many biological processes. Their elucidation is thus crucial to understand processes such as metabolic control, signal transduction, and gene regulation [1–6].

The list of PPIs provided by large-scale studies using for example yeast two-hybrid assays or mass spectrometry is increasing continuously [7–11].

Based on the large number of identified PPIs, it has become obvious that PPI networks are often controlled by posttranslational modification (PTM) of amino acids. One type of modification is the attachment of a functional group, such as methyl, acetyl, or phosphate. Another type of PTM is the attachment of an entire protein, like ubiquitin or SUMO (small ubiquitin-like modifier) to a lysine residue of the target protein.

These SUMO moieties mediate PPIs by recognizing short peptide stretches that were termed SUMO-interacting motifs (SIMs) or SUMO-binding motifs (SBMs). SUMO conjugation and interaction have been shown to be involved in various cellular processes, such as transcriptional regulation, cell cycle progression, DNA damage response, and signal transduction [12]. In eukaryotic cells, SIMs are also utilized for hostpathogen interactions [13], e.g., for anti-viral response [14].

In human cells, at least three SUMO paralogs (hSUMO1, 2, and 3) are expressed [15, 16]. The hSUMO2 and hSUMO3

Electronic supplementary material The online version of this article (doi:10.1007/s00894-015-2597-1) contains supplementary material, which is available to authorized users.

C. Jardin :A. H. C. Horn :H. Sticht (*)

Bioinformatik, Institut für Biochemie,

Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstr. 17, 91054 Erlangen, Germany e-mail:

J Mol Model (2015) 21:50

DOI 10.1007/s00894-015-2597-1 isoforms are almost identical and share ~50 % identity with hSUMO1 (Fig. 1).

Structural analyses of SUMO-SIM complexes have shown that all SIMs bind to a surface patch between theα-helix and a β-sheet of the SUMO protein and extend the β-sheet of SUMO by one additional strand. However, two different binding orientations are observed, in which the SIM either attaches as a parallel or an antiparallel strand to the SUMO β-sheet.

Structurally characterized examples of SIMs binding in an antiparallel orientation are the M-IR2 domain of RanBP2 [17], and the IR1 domain of RanBP2 [18]. The parallel binding mode is observed for the SIMs from PIASx [19], MCAF1 [20], and Daxx [21]. A very recent publication revealed that the ubiquitin ligase RNF2 recognizes a SUMO-dimer via two

SIM motifs. One of the motifs interacts in a parallel fashion with SUMO,while the second SIM concomitantly binds to the second SUMOmoiety in an antiparallel fashion [22]. Regardless of the orientation, binding is primarily mediated by a stretch of four residues containing 3–4 hydrophobic amino acids (I, V, or L). This core interaction motif is a common property of all SIMs, whereas the remaining sequence features exhibit a considerable variability. For example the stretch of hydrophobic residues may contain an insertion of a variable residue at either the second or the third position, like exemplified for the V-I-D-L motif present in the SIMs of the PIASx andMCAF1 proteins. Acidic residues were not only observed within the core motif but also in the flanking regions of the core motif [23] and were shown to enhance binding affinity due to interactions with basic residues of hSUMO on SIM interaction interface [21, 24, 25]. In addition, SIM binding may also be regulated by the phosphorylation of serine residues which allows a fine-tuning of the affinity of binding to hSUMO [21, 23, 26].

Several studies have also addressed the issue of binding specificity of SIMs for the different human SUMO paralogs.

Most SIMs investigated do not display a pronounced specificity for either hSUMO1 or hSUMO2 [23]. However, more recent work revealed several examples of hSUMO2/3specific SIMs [20, 27–29]. For the SIM sequence of the human Daxx protein, it has been additionally shown that phosphorylation promotes binding affinity toward hSUMO1 over hSUMO2/3 thus favoring an interaction with hSUMO1modified proteins [21]. The studies above indicate that despite striking common structural features, human SUMOs exhibit paralog-specific properties.