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Scaling theory generates transferable (even universal) algebraic and geometrical relations between the amino acid sequences and the aggregation functions of the three titled radically different proteins. In addition to the two hydropathicity scales and beta strand scales used in earlier p53 work, a second beta strand Hot Spot scale is shown to yield very accurate results for oligomerization of p53, the tumor suppressor. These algebraic and geometrical relations could be caused topologically by the dominance of protein-protein aggregation by interactions in a membrane catalytic surface layer.
Pathological folding and oligomer formation of the amyloid beta-protein (Abeta) are widely perceived as central to Alzheimers disease (AD). Experimental approaches to study Abeta self-assembly are problematic, because most relevant aggregates are qua
The flexibility in gap cost enjoyed by Hidden Markov Models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately ex
Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback-Leibler divergence (Dx) between protein co
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the validatio
To shorten the time required to find effective new drugs, like antivirals, a key parameter to consider is membrane permeability, as a compound intended for an intracellular target with poor permeability will have low efficacy. Here, we present a comp