Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly. Issue 21 (15th November 2022)

• Record Type: Journal Article
• Authors: Bhattacharya, Amrita; Shukla, Vaibhav Kumar; Kachariya, Nitin; Preeti, ; Sehrawat, Parveen; Kumar, Ashutosh
• Is Part Of: Journal of molecular biology. Volume 434:Issue 21(2022)
• Publication Date: 2022-11-15
• Subjects: Skp1 -- SCF complex -- protein Structure -- NMR Dynamics -- structural adaptability; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2022.167830
• Languages: English
• ISSNs: 0022-2836

Abstract

Graphical abstract: Highlights: The solution structure of free Skp1 reveals that the helices, particularly H8, are disordered in the unbound form. Structural conservation allows Cul-1 binding at the NTD (N-terminal domain) of Skp1, whereas structural plasticity allows different F-box recognition at the C-terminal helices of Skp1. Conformational sampling of excited sub-states by Skp1 residues, which are involved in F-box interactions, indicates that the excited state may be responsible for recruiting F-box proteins. Abstract: Skp1(S-phase kinase-associated protein 1 - Homo sapiens ) is an adapter protein of the SCF(Skp1-Cullin1-Fbox) complex, which links the constant components (Cul1-RBX) and the variable receptor (F-box proteins) in Ubiquitin E3 ligase. It is intriguing how Skp1 can recognise and bind to a variety of structurally different F-box proteins. For practical reasons, previous efforts have used truncated Skp1, and thus it has not been possible to track the crucial aspects of the substrate recognition process. In this background, we report the solution structure of the full-length Skp1 protein determined by NMR spectroscopy for the first time and investigate the sequence-dependent dynamics in the protein. The solution structure reveals that Skp1 has an architecture: β1-β2-H1-H2-L1–H3-L2-H4-H5-H6-H7(partially formed) and a long tail-like disordered C-terminus. Structural analysis using DALI (Distance Matrix Alignment) reveals conserved domain structure across species for Skp1. Backbone dynamics investigated using NMR relaxation suggest substantial variation in the motional timescales along the length of the protein. The loops and the C-terminal residues are highly flexible, and the (R2 /R1 ) data suggests μs-ms timescale motions in the helices as well. Further, the dependence of amide proton chemical shift on temperature and curved profiles of their residuals indicate that the residues undergo transitions between native state and excited state. The curved profiles for several residues across the length of the protein suggest that there are native-like low-lying excited states, particularly for several C-terminal residues. Our results provide a rationale for how the protein can adapt itself, bind, and get functionally associated with other proteins in the SCF complex by utilising its flexibility and conformational sub-states.