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Protein dynamics and molecular recognition at the crossroad between experiments and theory

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Despite the diffusion of physical and chemical techniques that allowed the investigation of molecular structures between the 50s and 70s, atomic level descriptions of macromolecular objects of biological interest remained rather elusive for a long period, leading to a very low number of protein structures ...

Despite the diffusion of physical and chemical techniques that allowed the investigation of molecular structures between the 50s and 70s, atomic level descriptions of macromolecular objects of biological interest remained rather elusive for a long period, leading to a very low number of protein structures deposited before the end of the 80s. However in the following years, this number grew dramatically due to the contemporary development of second and third generation synchrotron light sources and the diffusion of isotope labelling techniques and of higher field magnets, which respectively strongly encouraged the diffusion of X Rays Cristallography and NMR Spectroscopy as the leading techniques for the protein structure determination. If these techniques have been for the last decades able to provide an atomic level description of the spatial arrangement of biomacromolecules, more recently new approaches emerged for the study of larger structures (Cryo-Electron Microscopy), or of the spatial organization of oligomers (SAXS).

The aforementioned techniques offer a large set of possibilities to investigate biopolymeric structures and their interaction with each other (i.e. molecular recognition), which is the first step towards the comprehension of molecular recognition in physiologically relevant phenomena. However, only in the very last years the importance of dynamics and of the timescale of atomic and molecular motions emerged clearly, suggesting that a new era of reconsideration of both existing and new structures has begun and that a syncretic approach must be adopted in order to provide a novel vision of molecular recognition based on dynamic properties of biomolecules and on a temporal hierarchy of events.

Moreover in the recent years, a plethora of computational techniques, in particular the diffusion of molecular mechanics (MM) / dynamics (MD) based techniques (plain MD, Metadynamics, Accelerated MD, Langevin Dynamics, rigid body docking) reinforced the idea that the coupling between structure and dynamics is crucial for the explanation of physical-chemical properties of biomolecules and for the prediction of interactions between molecular partners in the living organisms. In particular, due to the availability of increasing computational power at relatively low cost, we assisted to the rise in importance of cross-contamination between computational and experimental disciplines in this sense. This led to the development of new disciplines that reject a straightforward classification and that face new challenges, with experimental data interpreted on the light of computational models or, vice versa, where the computational physical-chemistry is used as a generator of hypothesis verified by means of experimental techniques.

In this sense, our Research Topic intends to bring together current and interdisciplinary research, reviews, and opinions related to the big theme of molecular recognition of and between biomacromolecules, showing the strength of a crosstalk between experimental data and computational models. We cordially encourage authors from fields of biology, chemistry, physics, informatics, and other related disciplines to submit their manuscripts related to this Research Topic for publication.


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