Folding a Small Protein Using Harmonic Linear Discriminant Analysis

Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethora of enhanced sampling methods has been developed. One important class of such methods relies on the application of a bias that is function of a set of collective variables specially designed for the problem under consideration. The design of good collective variables can be challenging and thereby constitutes the main bottle neck in the application of these methods. To address this problem, recently we have introduced Harmonic Linear Discriminant Analysis, a method to systematically construct collective variables. The method uses as input information on the metastable states visited during the process that is being considered, information that can be gathered in short unbiased MD simulations, to construct the collective variables as linear combinations of a set of descriptors. Here, to scale up our examination of the method's efficiency, we applied it to the folding of Chignolin in water. Interestingly, already before any biased simulations were run, the constructed one dimensional collective variable revealed much of the physics that underlies the folding process. In addition, using it in Metadynamics we were able to run simulations in which the system goes from the folded state to the unfolded one and back, where to get fully converged results we combined Metadynamics with Parallel Tempering. Finally, we examined how the collective variable performs when different sets of descriptors are used in its construction

Optimization of a small molecule inhibitor of secondary nucleation in α-synuclein aggregation

Parkinson’s disease is characterised by the deposition in the brain of amyloid aggregates of α-synuclein. The surfaces of these amyloid aggregates can catalyse the formation of new aggregates, giving rise to a positive feedback mechanism responsible for the rapid proliferation of α-synuclein deposits. We report a procedure to enhance the potency of a small molecule to inhibit the aggregate proliferation process using a combination of in silico and in vitro methods. The optimized small molecule shows potency already at a compound:protein stoichiometry of 1:20. These results illustrate a strategy to accelerate the optimisation of small molecules against α-synuclein aggregation by targeting secondary nucleation

Guide for determination of protein structural ensembles by combining cryo-EM data with metadynamics.

Funder: Federation of European Biochemical Societies; Id: http://dx.doi.org/10.13039/100012623Funder: Bodossaki Foundation; Id: http://dx.doi.org/10.13039/501100002752Metadynamics electron microscopy metaInference (MEMMI) is an integrative structural biology method that enables a rapid and accurate characterization of protein structural dynamics at the atomic level and the error in the cryo-EM experimental data, even in cases where conformations are separated by high energy barriers. It achieves this by incorporating (a) cryo-electron microscopy electron density maps with (b) metadynamic-enhanced-sampling molecular dynamics. Here, I showcase the setup and analysis protocol of MEMMI, used to discover the atomistic structural ensemble and error in the cryo-EM electron density map of the fuzzy coat of IAPP, a fibril implicated in type II diabetes

Determination of intermediate state structures in the opening pathway of SARS-CoV-2 spike using cryo-electron microscopy.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19, a highly infectious disease that is severely affecting our society and welfare systems. In order to develop therapeutic interventions against this condition, one promising strategy is to target spike, the trimeric transmembrane glycoprotein that the virus uses to recognise and bind its host cells. Here we use a metainference cryo-electron microscopy approach to determine the opening pathway that brings spike from its inactive (closed) conformation to its active (open) one. The knowledge of the structures of the intermediate states of spike along this opening pathway enables us to identify a cryptic pocket that is not exposed in the open and closed states. These results underline the opportunities offered by the determination of the structures of the transient intermediate states populated during the dynamics of proteins to allow the therapeutic targeting of otherwise invisible cryptic binding sites

Accelerating the Calculation of Protein-Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables

ISSN:1549-9618ISSN:1549-962

Approximating free energy and committor landscapes in standard transition path sampling using virtual interface exchange

Transition path sampling (TPS) is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of TPS does not directly provide the free energy landscape nor the kinetics, which motivated the development of path sampling extensions, such as transition interface sampling (TIS), and the reweighted paths ensemble (RPE), that are able to simultaneously access both kinetics and thermodynamics. However, performing TIS is more involved than TPS, and still requires (some) insight in the reaction to define interfaces. While packages that can efficiently compute path ensembles for TIS are now available, it would be useful to directly compute the free energy from a single TPS simulation. To achieve this, we developed an approximate method, denoted Virtual Interface Exchange, that makes use of the rejected pathways in a form of waste recycling. The method yields an approximate reweighted path ensemble that allows an immediate view of the free energy landscape from a single TPS, as well as enables a full committor analysis.Comment: 10 figure

Water structure and dynamics in the hydration layer of a type III anti-freeze protein

\u3cp\u3eWe report on a molecular dynamics study on the relation between the structure and the orientational (and hydrogen bond) dynamics of hydration water around the ocean pout AFP III anti-freeze protein. We find evidence for an increasing tetrahedral structure from the area opposite to the ice binding site (IBS) towards the protein IBS, with the strongest signal of tetrahedral structure around the THR-18 residue of the IBS. The tetrahedral structural parameter mostly positively correlates with increased reorientation decay times. Interestingly, for several key (polar) residues that are not part of the IBS but are in its vicinity, we observe a decrease of the reorientation time with increasing tetrahedral structure. A similar anti-correlation is observed for the hydrogen-bonded water molecules. These effects are enhanced at a lower temperature. We interpret these results in terms of the structure-making and structure-breaking residues. Moreover, we investigate the tetrahedral structure and dynamics of waters at a partially dehydrated IBS, and for the protein adsorbed at the air-water interface. We find that the mutation changes the preferred protein orientation upon adsorption at an air-water interface. These results are in agreement with the water-air Vibration Sum Frequency Generation spectroscopic experiments showing a strongly reduced tetrahedral signal upon mutation at the IBS.\u3c/p\u3

Stability and growth mechanism of self-assembling putative antifreeze cyclic peptides

\u3cp\u3eCyclic peptides (CPs) that self-assemble in nanotubes can be candidates for use as antifreeze proteins. Based on the cyclic peptide sequence cyclo-[(l-LYS-d-ALA-l-LEU-d-ALA)\u3csub\u3e2\u3c/sub\u3e], which can stack into nanotubes, we propose a putative antifreeze cyclic peptide (AFCP) sequence, cyclo-[(l-LYS-d-ALA)\u3csub\u3e2\u3c/sub\u3e-(l-THR-d-ALA)\u3csub\u3e2\u3c/sub\u3e], containing THR-ALA-THR ice binding motifs. Using molecular dynamics simulations we investigate the stability of these cyclic peptides and their growth mechanism. Both nanotube sequences get more stable as a function of size. The relative stability of the AFCP sequence CPNT increases at sizes greater than a dimer by forming intermolecular THR side chain H-bonds. We find that, like the naturally occurring AF protein from spruce budworm (Choristoneura fumiferana), the THR distances of the AFCP's ice binding motif match the ice prism plane O-O distances, thus making the AFCP a suitable AF candidate. In addition, we investigated the nanotube growth process, i.e. the association/dissociation of a single CP to an existing AFCP nanotube, by Transition Path Sampling. We found a general dock-lock mechanism, in which a single CP first docks loosely before locking into place. Moreover, we identified several qualitatively different mechanisms for association, involving different metastable intermediates, including a state in which the peptide was misfolded inside the hydrophobic core of the tube. Finally, we find evidence for a mechanism involving non-specific association followed by 1D diffusion. Under most conditions, this will be the dominant pathway. The results yield insights into the mechanisms of peptide assembly, and might lead to an improved design of self-assembling antifreeze proteins.\u3c/p\u3