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.
An efficient, practical, and high yielding synthesis of (R)-2-methylpyrrolidine is described. The sequence allows for the scalable preparation of the target compound in just four synthetic steps and proceeds in 83% overall yield and >99% optical purity from readily available starting materials.
Specificity of the plant innate immune system is often conferred by resistance (R) proteins. Most R proteins contain leucine-rich repeats (LRRs), a central nucleotide-binding site (NBS) and a variable amino-terminal domain. The LRRs are mainly involved in recognition, whereas the amino-terminal domain determines signalling specificity. The NBS forms part of a nucleotide binding (NB)-ARC domain that presumably functions as a molecular switch. The conserved nature of NB-ARC proteins makes it possible to map mutations of R protein residues onto the crystal structures of related NB-ARC proteins, providing hypotheses for the functional roles of these residues. A functional model emerges in which the LRRs control the molecular state of the NB-ARC domain. Pathogen recognition triggers nucleotide-dependent conformational changes that might induce oligomerisation, thereby providing a scaffold for activation of downstream signalling components.