Abstract: Disclosed herein are designed heterodimer proteins, monomeric polypeptides capable of forming heterodimer proteins, protein scaffolds including such polypeptides, and methods for using the heterodimer proteins and subunit polypeptides for designing logic gates.

Abstract: Disclosed herein include methods, compositions, and kits suitable for use in winner-take-all neural network computation in mammalian cells. In some embodiments, de novo designed protein heterodimers and engineered viral proteases are combined to implement a synthetic protein circuit that performs winner-take-all neural network computation. The synthetic protein circuit can include modules that compute weighted sums of input protein concentrations through reversible binding interactions, and allow for self-activation and mutual inhibition of protein components using irreversible proteolytic cleavage reactions.

Abstract: Disclosed herein are designed heterodimer proteins, monomeric polypeptides capable of forming heterodimer proteins, protein scaffolds including such polypeptides, and methods for using the heterodimer proteins and subunit polypeptides for designing logic gates.

Abstract: The present disclosure provides a chimeric polypeptide comprising a helical bundle which comprises between about two and about seven alpha-helices and a bioactive peptide, wherein one or more of the alpha helices form one or more inter-helix hydrogen bonds and comprise at least one phosphorylation site and wherein the bioactive peptide is conformationally placed inside the helical bundle so that the bioactive peptide is not activated or exposed. The disclosure also provides a nucleotide sequence encoding the chimeric polypeptide, a vector comprising the nucleotide sequence, a cell comprising the nucleotide sequence, and method of making, using, or designing the chimeric polypeptide.

Abstract: Disclosed herein are polypeptides that serve as building blocks that can be used, for example, to design 2D protein arrays, methods for designing such polypeptides, and methods for their use.

Abstract: Disclosed herein are polypeptides or polypeptide oligomers, including a buried hydrogen bond network that includes at least (1, 2, 3, 4, 5, 6, 7, 8, or 9) pH sensitive amino acids located (i) at an intra-chain interface between different: structural elements in one polypeptide, or (it) at an inter-chain interface between structural elements present in different chains of a polypeptide oligomer, wherein the polypeptide or polypeptide oligomer is stable above a given pH, and wherein the polypeptide or polypeptide oligomer undergoes a conformational transition when subjected to a pH at or below the given pH.

Abstract: Disclosed herein are designed heterodimer proteins, monomeric polypeptides capable of forming heterodimer proteins, protein scaffolds including such polypeptides, and methods for using the heterodimer proteins and subunit polypeptides for designing logic gates.

Abstract: Disclosed herein are designed heterodimer proteins, monomeric polypeptides capable of forming heterodimer proteins, protein scaffolds including such polypeptides, and methods for using the heterodimer proteins and subunit polypeptides for designing logic gates.

Abstract: De novo designed multi-pass transmembrane polypeptides are described, that include 2 or more transmembrane domains that are each between 15 and 35 amino acids in length, include one or more polar residues, and include at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, or more hydrophobic amino acid residues.

Abstract: Disclosed herein are designed heterodimer proteins, monomeric polypeptides capable of forming heterodimer proteins, protein scaffolds including such polypeptides, and methods for using the heterodimer proteins and subunit polypeptides for designing logic gates.

Abstract: Methods and apparatus for identifying and screening hydrogen bond networks are provided. A computing device can determine a search space for hydrogen bond networks related to one or more molecules, where the search space can include a plurality of energy terms related to a plurality of residues related to the hydrogen bond networks. The computing device can search the search space to identify one or more hydrogen bond networks based on the plurality of energy terms. The computing device can screen the identified hydrogen bond networks to identity one or more screened hydrogen bond networks based on scores for the identified hydrogen bond networks. An output can be generated that is related to the one or more screened hydrogen bond networks. Also provided are polypeptides that can form homo-oligomers with modular hydrogen bond network-mediated specificity.

Abstract: Methods and apparatus for identifying and screening hydrogen bond networks are provided. A computing device can determine a search space for hydrogen bond networks related to one or more molecules, where the search space can include a plurality of energy terms related to a plurality of residues related to the hydrogen bond networks. The computing device can search the search space to identify one or more hydrogen bond networks based on the plurality of energy terms. The computing device can screen the identified hydrogen bond networks to identity one or more screened hydrogen bond networks based on scores for the identified hydrogen bond networks. An output can be generated that is related to the one or more screened hydrogen bond networks. Also provided are polypeptides that can form homo-oligomers with modular hydrogen bond network-mediated specificity.

Abstract: Methods and apparatus for identifying and screening hydrogen bond networks are provided. A computing device can determine a search space for hydrogen bond networks related to one or more molecules, where the search space can include a plurality of energy terms related to a plurality of residues related to the hydrogen bond networks. The computing device can search the search space to identify one or more hydrogen bond networks based on the plurality of energy terms. The computing device can screen the identified hydrogen bond networks to identity one or more screened hydrogen bond networks based on scores for the identified hydrogen bond networks. An output can be generated that is related to the one or more screened hydrogen bond networks. Also provided are polypeptides that can form homo-oligomers with modular hydrogen bond network-mediated specificity.