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

一种寡聚多肽、寡聚体的技术，应用在计算设备,计算机可读介质,蛋白质寡聚体,装置领域，能够解决极性氨基酸不能相互作用相互氢键结合能力等问题

Active Publication Date: 2022-04-29
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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Experimental program
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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. The computing device can determine a search space of a hydrogen bond network associated with one or more molecules, where the search space can include a plurality of energy terms associated with a plurality of residues involved in the hydrogen bond network. 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 may screen the identified hydrogen bonding networks based on the scores of the identified hydrogen bonding networks to identify one or more screened hydrogen bonding networks. Output related to one or more screened hydrogen bond networks can be generated. Also provided are polypeptides that can form homo-oligomers with specificity mediated by modular hydrogen bond networks.

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 Patents(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