Context-dependent contributions of backbone hydrogen bonding to ß-sheet folding energetics

Deechongkit, Songpon; Nguyen, Houbi; Powers, Evan T.; Dawson, Philip E.; Gruebele, Martin; Kelly, Jeffery W.
July 2004
Nature;7/1/2004, Vol. 430 Issue 6995, p101
Academic Journal
Backbone hydrogen bonds (H-bonds) are prominent features of protein structures; however, their role in protein folding remains controversial because they cannot be selectively perturbed by traditional methods of protein mutagenesis. Here we have assessed the contribution of backbone H-bonds to the folding kinetics and thermodynamics of the PIN WW domain, a small ß-sheet protein, by individually replacing its backbone amides with esters. Amide-to-ester mutations site-specifically perturb backbone H-bonds in two ways: a H-bond donor is eliminated by replacing an amide NH with an ester oxygen, and a H-bond acceptor is weakened by replacing an amide carbonyl with an ester carbonyl. We perturbed the 11 backbone H-bonds of the PIN WW domain by synthesizing 19 amide-to-ester mutants. Thermodynamic studies on these variants show that the protein is most destabilized when H-bonds that are enveloped by a hydrophobic cluster are perturbed. Kinetic studies indicate that native-like secondary structure forms in one of the protein's loops in the folding transition state, but the backbone is less ordered elsewhere in the sequence. Collectively, our results provide an unusually detailed picture of the folding of a ß-sheet protein.


Related Articles

  • Mutational analysis of kinetic partitioning in protein folding and protein–DNA binding. Sánchez, Ignacio E.; Ferreiro, Diego U.; de Prat Gay, Gonzalo // PEDS: Protein Engineering, Design & Selection;Jan2011, Vol. 24 Issue 1/2, p179 

    Kinetic partitioning between competing routes is present in many biological processes. Here, we propose a methodology to characterize kinetic partitioning through site-directed mutagenesis and apply it to parallel routes for unfolding of the TI I27 protein and for recognition of its target DNA...

  • Folding at the speed limit. Yang, Wei Yuan; Gruebele, Martin // Nature;5/8/2003, Vol. 423 Issue 6936, p193 

    Many small proteins seem to fold by a simple process explicable by conventional chemical kinetics and transition-state theory. This assumes an instant equilibrium between reactants and a high-energy activated state[SUP1]. In reality, equilibration occurs on timescales dependent on the molecules...

  • Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins. Jianmin Gao; Bosco, Daryl A.; Powers, Evan T.; Kelly, Jeffery W. // Nature Structural & Molecular Biology;Jul2009, Vol. 16 Issue 7, p684 

    The energetic contributions of hydrogen bonding to protein folding are still unclear, despite more than 70 years of study. This is due partly to the difficulty of extracting thermodynamic information about specific interactions from protein mutagenesis data and partly to the context dependence...

  • The Rubik’s cube problem revisited: a statistical thermodynamic approach. Lee, C.-L.; Huang, M.-C. // European Physical Journal B -- Condensed Matter;Jul2008, Vol. 64 Issue 2, p257 

    Inspired by the protein folding problem, we propose a Rubik’s cube model and study its thermodynamic and kinetic behavior. We find that the energy landscape contains a tiny funnel-like region, as the dynamics towards the native state is mostly diffusive. In particular, from Monte Carlo...

  • Thermodynamics and kinetics of folding of a small peptide. Hansmann, Ulrich H. E.; Onuchic, Jose N. // Journal of Chemical Physics;7/15/2001, Vol. 115 Issue 3 

    We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at suitable temperatures. The results of these canonical...

  • Stable folding intermediates prevent fast interconversion between the closed and open states of Mad2 through its denatured state. Yuanyuan Zhao; Lianghui Li; Chunfei Wu; Xiaoyong Jiang; Baosheng Ge; Hao Ren; Fang Huang // PEDS: Protein Engineering, Design & Selection;Jan2016, Vol. 29 Issue 1, p23 

    Different states of metamorphic proteins can interconvert under physiological conditions to realize corresponding functions. The mechanism behind the conversion is critical for understanding how these proteins work. We report a combined thermodynamic and kinetic study on the folding/unfolding...

  • Effects of Knots on Protein Folding Properties. Soler, Miguel A.; Faísca, Patrícia F. N. // PLoS ONE;Sep2013, Vol. 8 Issue 9, p1 

    This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may...

  • A one-dimensional free energy surface does not account for two-probe folding kinetics of protein α3D. Feng Liu; Dumont, Charles; Yongjin Zhu; DeGrado, William F.; Feng Gai; Gruebele, Martin // Journal of Chemical Physics;2/14/2009, Vol. 130 Issue 6, pN.PAG 

    We present fluorescence-detected measurements of the temperature-jump relaxation kinetics of the designed three-helix bundle protein α3D taken under solvent conditions identical to previous infrared-detected kinetics. The fluorescence-detected rate is similar to the IR-detected rate only at...

  • Mutational investigation of protein folding transition states by Φ-value analysis and beyond: lessons from SH3 domain folding. Zarrine-Afsar, Arash; Sung Lun Lin; Neudecker, Philipp // Biochemistry & Cell Biology;Apr2010, Vol. 88 Issue 2, p231 

    Understanding how proteins adopt their unique native structures requires a complete structural characterization of the rate-limiting transition state(s) along the folding pathway. By definition, transition states are not significantly populated and are only accessible via folding kinetics...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics