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Rational design also tests our understanding of the principles underlying protein recognition.
Domain swapping has been shown to be an important mechanism controlling multiprotein assembly and has been suggested recently as a possible mechanism underlying protein aggregation.
Major advances in understanding fundamental principles underlying protein folding in optimized in vitro conditions have yielded detailed physicochemical principles of folding landscapes for small, single domain proteins.
To successfully design new proteins and understand the effects of mutations in natural proteins, we must understand the geometric and physicochemical principles underlying protein structure.
This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding.
Here we review representative studies utilizing such an integrated real-time structural approach designed to reveal molecular mechanisms underlying protein interactions at atomic resolution.
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The de novo design of protein-protein interfaces is a stringent test of our understanding of the principles underlying protein-protein interactions and would enable unique approaches to biological and medical challenges.
Presumably, this conformational constraint was accomplished by underlying protein-protein interactions, as modeled during the design of this epitope-scaffold combination.
To date, such novel DNA binding sites have not been identified in any RecA family protein, and the mechanisms underlying protein-DNA and ssDNA-dsDNA interactions are not clear.
Finally, we use the model to predict the effects of changes in the topology of the underlying protein-interaction network.
Here, we studied the dynamics of telomere length by integrating the underlying protein-counting mechanism into a stochastic model.
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