hypothesized that we could use them to design PPIs by targeting sites using only structural information from the target protein. To address the de novo PPI design problem, we devised a three-stage computational approach depicted in Fig.1: (1) prediction of target buried interface sites with high...
hypothesized that we could use them to design PPIs by targeting sites using only structural information from the target protein. To address the de novo PPI design problem, we devised a three-stage computational approach depicted in Fig.1: (1) prediction of target buried interface sites with high...
However, the underlying structural principles governing such heterochiral protein–protein interactions remain largely unknown. In this study, we present the de novo design of-proteins consisting of 50–65 residues, aiming to target specific surface regions of-proteins or-peptides. Our designer-protein...
Here we explore the possibility of designing switchable protein systems de novo, through the modulation of competing inter- and intramolecular interactions. We design a static, five-helix ‘cage’ with a single interface that can interact either intramolecularly with a terminal ‘latch’ helix or ...
Recent advances in the field of de novo protein design are examined. The data are examined with respect to the hypothesis that most designed proteins exhibit characteristics similar to those of molten globules. Continuing efforts to produce novel proteins with the specific interactions that define natu...
Protein design aims to identify new protein sequences of desirable structure and biological function. Most current de novo protein design methods rely on physics-based force fields to search for low free-energy states following Anfinsen's thermodynamic hypothesis. A major obstacle of such approaches ...
De novo protein design can now generate binders with high affinity and specificity to structured proteins. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for ...
Metals Coordinate Protein–Protein Interactions chemistrydenovodesignmetalcoordinationproteinstructuresprotein–When Protein met Metal: The ability of metal ions to coordinate the assembly of specific ... Kagan,Kerman,Heinz-Bernhard,... - 《Angewandte Chemie International Edition》 被引量: 16发表: 2008...
AlphaFold accurately predicts distinct conformations based on oligomeric state of a de novo designed protein Using the molecular modeling program Rosetta, we designed a de novo protein, called SEWN0.1, that binds the heterotrimeric G protein G伪q. The design is he... MC Cummins,T Jacobs,FD ...
protein engineering as it could enable the construction of switchable nanomaterials, cooperatively activated biosensors and molecular machines that perform work by means of coordinated movements among their components. Previous work on the de novo design of allostery has demonstrated coupling between two ...