PubMed · 8016331
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F Arisaka. 1994. [Protein-protein interaction].. https://pubmed.ncbi.nlm.nih.gov/8016331/
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In 1978, for my PhD, I developed the efficient O(n3) dynamic programming algorithm for the-then open problem of RNA secondary structure prediction. This algorithm, now dubbed the "Nussinov algorithm", "Nussinov plots", and "Nussinov diagrams", is still taught across Europe and the U.S. As sequences started coming out in the 1980s, I started seeking genome-encoded functional signals, later becoming a bioinformatics trend. In the early 1990s I transited to proteins, co-developing a powerful computer vision-based docking algorithm. In the late 1990s, I proposed the foundational role of conformational ensembles in molecular recognition and allostery. At the time, conformational ensembles and free energy landscapes were viewed as physical properties of proteins but were not associated with function. The classical view of molecular recognition and binding was based on only two conformations captured by crystallography: open and closed. I proposed that all conformational states preexist. Proteins always have not one folded form-nor two-but many folded forms. Thus, rather than inducing fit, binding can work by shifting the ensembles between states, and this shifting, or redistributing the ensembles to maintain equilibrium, is the origin of the allosteric effect and protein, thus cell, function. This transformative paradigm impacted community views in allosteric drug design, catalysis, and regulation. Dynamic conformational ensemble shifts are now acknowledged as the origin of recognition, allostery, and signaling, underscoring that conformational ensembles-not proteins-are the workhorses of the cell, pioneering the fundamental idea that dynamic ensembles are the driving force behind cellular processes. Nussinov was recognized as pioneer in molecular biology by JMB.
Neutron and X-ray small-angle scattering techniques have made significant advances in their applications in structural molecular biology. They have become important tools for studying the structural basis for biomolecular function, revealing details of protein and DNA structure, as well as functionally important conformational flexibility and interactions. More powerful neutron and X-ray sources are now available which enable faster data acquisition on lower concentration samples, as well as time-resolved studies in the case of synchrotron sources. This source development has been accompanied by instrument development and advances in scattering techniques. At the same time, advances in molecular biology that facilitate preparation of samples have made available more biological molecules suitable for study by scattering techniques. In this review we briefly describe the basic theory and practice of small-angle scattering and follow with examples of its application to studying the conformations of biomolecules in solution, as well as within functional complexes.
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