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Cooperative propagation of local stability changes from low-stability and high-stability regions in a SH3 domain.

Casares S, López-Mayorga O, Vega MC, Cámara-Artigas A, Conejero-Lara F
Proteins 67 531-47 (2007)
Related entries: 2cdt, 2f2w, 2f2x

Cited: 11 times
EuropePMC logo PMID: 17330285

Abstract

Site-directed mutagenesis has been used to produce local stability changes at two regions of the binding site surface of the alpha-spectrin SH3 domain (Spc-SH3) differing in their intrinsic stability. Mutations were made at residue 56, located at the solvent-exposed side of the short 3(10) helix, and at residue 21 in the tip of the flexible RT-loop. NMR chemical-shift analysis and X-ray crystallography indicated negligible changes produced by the mutations in the native structure limited to subtle rearrangements near the mutated residue and at flexible loops. Additionally, mutations do not alter importantly the SH3 binding site structure, although produce significant changes in its affinity for a proline-rich decapeptide. The changes in global stability measured by differential scanning calorimetry are consistent the local energy changes predicted by theoretical models, with the most significant effects observed for the Ala-Gly mutations. Propagation of the local stability changes throughout the domain structure has been studied at a per-residue level of resolution by NMR-detected amide hydrogen-deuterium exchange (HX). Stability propagation is remarkably efficient in this small domain, apparently due to its intrinsically low stability. Nevertheless, the HX-core of the domain is not fully cooperative, indicating the existence of co-operative subunits within the core, which is markedly polarized. An equilibrium phi-analysis of the changes in the apparent Gibbs energies of HX per residue produced by the mutations has allowed us to characterize structurally the conformational states leading to HX. Some of these states resemble notably the folding transition state of the Spc-SH3 domain, suggesting a great potential of this approach to explore the folding energy landscape of proteins. An energy perturbation propagates more effectively from a flexible region to the core than in the opposite direction, because the former affects a broader region of the energy landscape than the latter. This might be of importance in understanding the special thermodynamic signature of the SH3-peptide interaction and the relevance of the dual character of SH3 binding sites.

Articles - 2f2v mentioned but not cited (2)

  1. Conformational and functional analysis of molecular dynamics trajectories by self-organising maps. Fraccalvieri D, Pandini A, Stella F, Bonati L. BMC Bioinformatics 12 158 (2011)
  2. Ultratight crystal packing of a 10 kDa protein. Trillo-Muyo S, Jasilionis A, Domagalski MJ, Chruszcz M, Minor W, Kuisiene N, Arolas JL, Solà M, Gomis-Rüth FX. Acta Crystallogr D Biol Crystallogr 69 464-470 (2013)


Reviews citing this publication (2)

  1. Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains. Zafra-Ruano A, Luque I. FEBS Lett 586 2619-2630 (2012)
  2. Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain. Cámara-Artigas A. Arch Biochem Biophys 602 116-126 (2016)

Articles citing this publication (7)

  1. Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins. Morra G, Colombo G. Proteins 72 660-672 (2008)
  2. A single mutation in an SH3 domain increases amyloid aggregation by accelerating nucleation, but not by destabilizing thermodynamically the native state. Varela L, Morel B, Azuaga AI, Conejero-Lara F. FEBS Lett 583 801-806 (2009)
  3. Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications. Ortega Roldan JL, Casares S, Ringkjøbing Jensen M, Cárdenes N, Bravo J, Blackledge M, Azuaga AI, van Nuland NA. PLoS One 8 e73018 (2013)
  4. Solution structure, dynamics and thermodynamics of the three SH3 domains of CD2AP. Roldan JL, Blackledge M, van Nuland NA, Azuaga AI. J Biomol NMR 50 103-117 (2011)
  5. Detection of native-state nonadditivity in double mutant cycles via hydrogen exchange. Boyer JA, Clay CJ, Luce KS, Edgell MH, Lee AL. J Am Chem Soc 132 8010-8019 (2010)
  6. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors. Zafra Ruano A, Cilia E, Couceiro JR, Ruiz Sanz J, Schymkowitz J, Rousseau F, Luque I, Lenaerts T. PLoS Comput Biol 12 e1004938 (2016)
  7. Evaluation of folding co-operativity of a chimeric protein based on the molecular recognition between polyproline ligands and SH3 domains. Candel AM, Cobos ES, Conejero-Lara F, Martinez JC. Protein Eng Des Sel 22 597-606 (2009)


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