The role of conformational selection in the molecular recognition of the wild type and mutants XPA67-80 peptides by ERCC1

The nucleotide excision repair proteins through the lens of molecular dynamics simulations

Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.

Binding Free Energies of Conformationally Disordered Peptides Through Extensive Sampling and End-Point Methods

The ability to obtain binding free energies from molecular simulation techniques provides a valuable support to the interpretation and design of experiments. Among all methods available, the most widely used equilibrium free energy methods range from highly accurate and computationally expensive perturbation theory-based methods, such as free energy perturbation (FEP), or thermodynamic integration (TI), through end-point methods, such as molecular mechanics with generalized Born and surface area solvation (MM/GBSA) or MM/PBSA, when the Poisson-Boltzmann method is used instead of GB, and linear interaction energy (LIE) methods, to scoring functions, which are relatively simple empirical functions widely used as part of molecular docking protocols. Because the use of FEP and TI approaches is restricted to cases where the perturbation leading from an initial to final state is negligible or minimal, their application to cases where large conformational changes are involved between bound and unbound states is rather complex, if not prohibitive in terms of convergence. Here we describe a protocol that involves the use of extensive conformational sampling through molecular dynamics (MD) in combination with end-point methods (MM/GB(PB)SA) with an additional quasi-harmonic entropy component, for the calculation of the relative binding free energies of highly flexible, or intrinsically disordered, peptides to a structured receptor.

Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly

Lack of structure is often an essential functional feature of protein domains. The coordination of macromolecular assemblies in DNA repair pathways is yet another task disordered protein regions are highly implicated in. Here I review the available experimental and computational data and within this context discuss the functional role of structure and disorder in one of the essential scaffolding proteins in the nucleotide excision repair (NER) pathway, namely Xeroderma pigmentosum complementation group A (XPA). From the analysis of the current knowledge, in addition to protein–protein docking and secondary structure prediction results presented for the first time herein, a mechanistic framework emerges, where XPA builds the NER pre-incision complex in a modular fashion, as “beads on a string”, where the protein–protein interaction “beads”, or modules, are interconnected by disordered link regions. This architecture is ideal to avoid the expected steric hindrance constraints of the DNA expanded bubble. Finally, the role of the XPA structural disorder in binding affinity modulation and in the sequential binding of NER core factors in the pre-incision complex is also discussed.