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Polypeptides capable of forming homo-oligomers with modular hydrogen bond network-mediated specificity and their design

A technology of hydrogen bonding and network, applied in the field of computer readable media, computing equipment, protein oligomers, and devices, can solve the problems of polar amino acids that cannot interact with each other, such as hydrogen bonding capabilities

Active Publication Date: 2019-02-05
UNIV OF WASHINGTON
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

In proteins, these challenges are compounded because backbone geometry is highly variable and polar amino acid pairs are often unable to interact to fully satisfy their mutual hydrogen bonding capacity

Method used

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  • Polypeptides capable of forming homo-oligomers with modular hydrogen bond network-mediated specificity and their design
  • Polypeptides capable of forming homo-oligomers with modular hydrogen bond network-mediated specificity and their design
  • Polypeptides capable of forming homo-oligomers with modular hydrogen bond network-mediated specificity and their design

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Embodiment

[0255] Modularity and predictability of DNA interaction specificity are at the heart of molecular biology manipulation and DNA nanotechnology, but there is no similarity in nature, and how to achieve similar programmable specificity with proteins is unclear. There are more polar amino acids than DNA bases, and each amino acid can adopt multiple side chain conformations in different backbone environments, enabling countless network possibilities. The inventors have developed a general computing method, the development of HBNet TM To quickly enumerate all possible side chain hydrogen bond networks in the input backbone structure (Figure IA).

[0256] Traditional protein design algorithms are not well suited for this purpose, since the total system energy usually represents the sum of interactions between pairs of residues used to calculate efficiencies, and thus cannot clearly disconnect a connected hydrogen bond network from a set of separate the hydrogen bonds. HBNet TM Fir...

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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, wherein 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.

Description

[0001] related application [0002] This application claims priority to US Provisional Patent Application Serial No. 62 / 317,190, filed April 1, 2016, which is hereby incorporated by reference in its entirety. Background technique [0003] Hydrogen bonding plays a key role in the structure, function and interaction specificity of biomolecules. There are two major challenges in designing de novo hydrogen-bonding interactions: first, hydrogen-bonding atoms are geometrically constrained within a narrow range of directions and distances; second, almost all polar atoms must interact with other macromolecular polar atoms or with solvents. Participate in hydrogen bonds together, otherwise there would be a considerable energy loss in dehydration during folding or binding. The DNA double helix neatly addresses both challenges; pairs of bases come together such that all buried polar atoms form self-contained hydrogen bonds between the two bases and have a near-ideal geometry. In protei...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C07K1/113C07K2/00C07K14/00C07K14/435C07K16/18G01N33/48C12N15/11
CPCC07K1/113C07K14/001G16B15/20C07K2/00C07K14/435C07K16/18
Inventor D·贝克尔S·博伊肯Z·陈C·许S·贝米欧R·兰根
Owner UNIV OF WASHINGTON
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