Small Peptide Binding Stiffens the Ubiquitin-like Protein SUMO1

Kotamarthi, Hema Chandra; Yadav, Anju; Ainavarapu, Sri Rama Koti

doi:10.1016/j.bpj.2014.11.3474

Cited by 16 publications

(22 citation statements)

References 34 publications

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“…37,43,70 From the free energy plots in Figure 6(b) it is possible to estimate such a spring constant of the protein along the direction of pulling, using a method described previously. 70 Assuming that the free energy is quadratic in the extension between the two ends: 68 and D may thus be highly dependent on the pulling direction.…”

Section: Discussionmentioning

confidence: 99%

“…37 Here, we demonstrate that protein softness can be tuned through the rational inclusion of salt bridges in the protein.…”

Section: Figurementioning

confidence: 99%

“…38,42,[45][46][47] The Ainavarapu group used this technique to show that the protein SUMO I can withstand less deformation before unfolding, exhibiting a reduction in mechanical softness upon the binding of a small polypeptide ligand. 37 A recent survey of the experimental literature on the mechanical unfolding of proteins showed a robust correlation between F U x U with mechanically strong proteins (large F U x U , and mechanically weak proteins (small F U x U 48 . Using this SMFS approach to measure the impact of specific non-covalent interactions on the mechanical properties, F U x U, has the potential to uncover the 'design features' of extreme-adapted proteins.…”

Section: Introductionmentioning

confidence: 99%

“…In the last decade this technique has provided valuable insight into the impact of specific structural adaptations on protein mechanical stability. [32][33][34][35][36][37][38][39][40][41][42][43] For example, studies have determined the importance of interactions between residues distal in sequence, 41 packing in the hydrophobic core of a proteins, 40 the role of hydrogen bonds 44 , solvent accessibility of hydrogen bonds, 45 non-native interactions as well as the identification of strong and weak sequence motifs in protein families. 38,42,[45][46][47] The Ainavarapu group used this technique to show that the protein SUMO I can withstand less deformation before unfolding, exhibiting a reduction in mechanical softness upon the binding of a small polypeptide ligand.…”

Section: Introductionmentioning

confidence: 99%

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Tuning protein mechanics through an ionic cluster graft from an extremophilic protein

et al. 2016

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Proteins from extremophilic organisms provide excellent model systems to determine the role of non-covalent interactions in defining protein stability and dynamics as well as being attractive targets for the development of robust biomaterials. Hyperthermophilic proteins have a prevalence of salt bridges, relative to their mesophilic homologues, which are thought to be important for enhanced thermal stability. However, the impact of salt bridges on the mechanical properties of proteins is far from understood. Here, a combination of protein engineering, biophysical characterisation, single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations directly investigates the role of salt bridges in the mechanical stability of two cold shock proteins; BsCSP from the mesophilic organism Bacillus subtilis and TmCSP from the hyperthermophilic organism Thermotoga maritima. Single molecule force spectroscopy shows that at ambient temperatures TmCSP is mechanically stronger yet, counter-intuitively, its native state can withstand greater deformation before unfolding (i.e. it is mechanically soft) compared with BsCSP. MD simulations were used to identify the location and quantify the population of salt bridges, and reveal that TmCSP contains a larger number of highly occupied salt bridges than BsCSP. To test the hypothesis that salt-bridges endow these mechanical properties on the hyperthermophilic CSP, a charged triple mutant (CTM) variant of BsCSP was generated by grafting an ionic cluster from TmCSP into the BsCSP scaffold. As expected CTM is thermodynamically more stable and mechanically softer than BsCSP. We show that a grafted ionic cluster can increase the mechanical softness of a protein and speculate that it could provide a mechanical recovery mechanism and that it may be a design feature applicable to other proteins.

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Section: Discussionmentioning

confidence: 99%

“…37 Here, we demonstrate that protein softness can be tuned through the rational inclusion of salt bridges in the protein.…”

Section: Figurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Tuning protein mechanics through an ionic cluster graft from an extremophilic protein

et al. 2016

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“…In this vein, the mechanical properties of protein G are substantially increased upon binding the IgG antibody 26 . Furthermore, SUMO1 increases its mechanical stability upon binding small peptides 27 . Similarly, the attachment of the short hydrophobic APPY polypeptide induces selective increase of the mechanical properties of the domain I of the multidomain DnaJ chaperone 28 .…”

Section: Toc Graphicsmentioning

confidence: 99%

DNA Binding Induces a Nanomechanical Switch in the RRM1 Domain of TDP-43

Wang

Rico-Lastres

Lezamiz

et al. 2018

J. Phys. Chem. Lett.

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Understanding the molecular mechanisms governing protein-nucleic acid interactions is fundamental to many nuclear processes. However, how nucleic acid binding affects the conformation and dynamics of the substrate protein remains poorly understood. Here we use a combination of single molecule force spectroscopy AFM and biochemical assays to show that the binding of TG-rich ssDNA triggers a mechanical switch in the RRM1 domain of TDP-43, toggling between an entropic spring devoid of mechanical stability and a shock absorber bound-form that resists unfolding forces of ∼40 pN. The fraction of mechanically resistant proteins correlates with an increasing length of the TG oligonucleotide, demonstrating that protein mechanical stability is a direct reporter of nucleic acid binding. Steered molecular dynamics simulations on related RNA oligonucleotides reveal that the increased mechanical stability fingerprinting the holo-form is likely to stem from a unique scenario whereby the nucleic acid acts as a "mechanical staple" that protects RRM1 from mechanical unfolding. Our approach highlights nucleic acid binding as an effective strategy to control protein nanomechanics.

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Protein nanomechanics in biological context

Alegre-Cebollada

2021

Biophys Rev

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How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.

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Small Peptide Binding Stiffens the Ubiquitin-like Protein SUMO1

Cited by 16 publications

References 34 publications

Tuning protein mechanics through an ionic cluster graft from an extremophilic protein

Tuning protein mechanics through an ionic cluster graft from an extremophilic protein

DNA Binding Induces a Nanomechanical Switch in the RRM1 Domain of TDP-43

Protein nanomechanics in biological context

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