The project has addressed the following areas in the past year: 1. Misfolding in multidomain proteins. We are working on the susceptibility of different protein folds to intramolecular domain-swapped misfolding using coarse-grained models. We are able to reproduce general trends (which proteins are known to misfold and which are known not to do so). We have developed a model for the formation of the misfolded states which explains the tendency to misfold in terms of a folding funnel. We are currently preparing a manuscript on these results. 2. Folding of membrane proteins. We are investigating the folding of membrane proteins using two lines of attack. The first is the development of an implicit membrane model based on the coarse-grained Martini force field. We already have very promising results for peptide insertion and assembly, and we are further refining the parameters. Secondly, we are taking a more brute force approach to determine how well atomistic force fields can fold and assemble membrane proteins. Here, the main obstacle is the membrane viscosity which is 2-3 orders of magnitude larger than that of water at 300 K. We have overcome this to a large extent by using a solute tempering replica exchange approach, which shows that force fields are predictive of membrane protein folds. 3. Force field development. A common problem with the energy functions used to simulate proteins is that unfolded and disordered states are too collapsed. We have resolved this problem by modifying the protein-water interactions directly, using experimental data for parametrization. Using the new parameters, we (and other independent groups) have obtained very promising results for the dimensions of unfolded proteins and association of peptides and proteins. These results are described in Ref. 1 of this report. 4. An accurate description of the water model is very important for capturing many biomolecular properties. We have shown that using an accurate water model, we are able to capture a very subtle effect of pressure on the stability of alpha helices, while using a commonly used water model gives qualitatively the wrong result (Ref. 2). 5. In collaboration with Ben Schuler, we have developed and validated a force field for chromophores in FRET experiments, and validated it by comparison with time-resolved anisotropy data, FRET efficiencies for model systems, and data for bimolecular association of the chromophores with tryptophan. We anticipate that this model should prove more useful for interpretation of experiments than force fields developed by standard methods (Ref 3). This chromophore force field has been applied in preliminary form to investigate the effects of chromophores on unfolded proteins (Ref. 4). 6. A key unresolved aspect of protein folding dynamics is the contribution of interactions within the chain to slowing folding, known as 'internal friction'. Building on our previous results where we showed that a common origin for internal friction in all proteins is crossing of local torsional barriers in the energy landscape, we have developed a simple model to explain explain the variation in internal friction from protein to protein (Ref. 5). We are now working on interpreting internal friction in unfolded and disordered chains. 7. In collaboration with David de Sancho (Cambridge) and Jochen Blumberger (University College London) we have been investigating the diffusion of gas molecules to the active sites of hydrogenase enzymes. The methodology we have developed (Ref. 6) should be generally applicable to study diffusion of any substrate molecules within enzymes, and will be combined with a description of the chemical step of binding to obtain a complete picture of the binding kinetics and mechanism. 8. We are initiating a project in collaboration with Tuomas Knowles in Cambridge in order to describe the formation of amyloid fibers, and in particular the molecular mechanism of secondary nucleation. We are taking two-approaches. The first is to build a simple coarse-grained model based on the known structure of the fiber. The second is to characterise the affinity, association rate and binding mode of the peptides with the surface of an existing fiber, which can be checked against SPR data from the Knowles lab. 9. In collaboration with Ad Bax, we have characterized the effect of pressure on HIV-1 protease. We have shown that modest pressure drives a structural transition of the protease from a structure with active-site flaps closed to one where they are open. This work has just been accepted for publication (Ref. 7). 10. In collaboration with Rob Tycko and Victor Muoz (UC Merced), we are using temperature-dependent chemical shifts for an unfolded protein (the villin headpiece subdomain) to benchmark the quality of force-fields for reproducing unfolded state properties.
| Zheng, Wenwei; Best, Robert B (2018) An Extended Guinier Analysis for Intrinsically Disordered Proteins. J Mol Biol 430:2540-2553 |
| Zheng, Wenwei; Zerze, Gül H; Borgia, Alessandro et al. (2018) Inferring properties of disordered chains from FRET transfer efficiencies. J Chem Phys 148:123329 |
| Tian, Pengfei; Louis, John M; Baber, James L et al. (2018) Co-Evolutionary Fitness Landscapes for Sequence Design. Angew Chem Int Ed Engl 57:5674-5678 |
| Borgia, Alessandro; Borgia, Madeleine B; Bugge, Katrine et al. (2018) Extreme disorder in an ultrahigh-affinity protein complex. Nature 555:61-66 |
| Meng, Fanjie; Bellaiche, Mathias M J; Kim, Jae-Yeol et al. (2018) Highly Disordered Amyloid-? Monomer Probed by Single-Molecule FRET and MD Simulation. Biophys J 114:870-884 |
| Best, Robert B (2018) Race to the native state. Proc Natl Acad Sci U S A 115:2267-2269 |
| De Sancho, David; Schönfelder, Jörg; Best, Robert B et al. (2018) Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force. J Phys Chem B : |
| Dignon, Gregory L; Zheng, Wenwei; Kim, Young C et al. (2018) Sequence determinants of protein phase behavior from a coarse-grained model. PLoS Comput Biol 14:e1005941 |
| Best, Robert B; Lindorff-Larsen, Kresten (2018) Editorial overview: Theory and simulation: Interpreting experimental data at the molecular level. Curr Opin Struct Biol 49:iv-v |
| Doma?ski, Jan; Sansom, Mark S P; Stansfeld, Phillip J et al. (2018) Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association. J Chem Theory Comput 14:1706-1715 |
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