Combined computational and structural studies to create novel macromolecular recognition properties

结合计算和结构研究来创造新的大分子识别特性

• 批准号: 10543489
• 负责人: BARRY L. STODDARD
• 金额: $ 35.2万
• 依托单位: FRED HUTCHINSON CANCER CENTER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-04-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10543489
• 关键词: Affinity; Algorithms; Amino Acid Sequence; Base Pairing; Behavior; Binding; Binding Proteins; Binding Sites; Biochemical; Biological; Blinded; Collaborations; Complex; Complex Mixtures; Computer Analysis; Computer Models; Crystallography; DNA; DNA Binding; DNA-Binding Proteins; Dissection; Docking; Drug Design; Electrostatics; Engineering; Equilibrium; Hybrids; Hydrogen Bonding; Ligand Binding; Ligands; Modeling; Molecular; Motivation; Mutagenesis; Performance; Process; Property; Protein Conformation; Protein Engineering; Proteins; Protocols documentation; Resolution; Reverse engineering; Running; Sampling; Scaffolding Protein; Series; Solvents; Specificity; Structure; Surface; System; Tandem Repeat Sequences; Testing; Variant; Work; X-Ray Crystallography; data resource; design; design verification; improved; novel; pressure; protein complex; protein folding; protein structure; small molecule; statistical and machine learning

PROJECT SUMMARY The design of macromolecular binding interactions and complexes, and corresponding alteration of binding specificity, is a challenging endeavor that remains recalcitrant to computational approaches. This is true both for the creation of protein-protein complexes (which are driven by a enthalpic changes established primarily by stereochemical complementarity, balanced against large competing entropic changes) and for the redesign of protein-DNA complexes (which are heavily dependent upon DNA bending, hydrogen-bonds, electrostatic contacts, and the presence of solvent and counterions throughout the molecular interface). Over the past several years we have collaborated with several computational groups to help develop and validate computational approaches for the design and optimization of protein-protein recognition, protein-DNA recognition, and protein-small molecule recognition. Those studies have contributed to several new computational engineering approaches, including hybrid strategies that combine ab initio design of protein folds and binding sites, the ‘Rotamer Interaction Feld’ (RIF) docking protocol for efficient sampling of protein sequence and conformation, and novel parametric design approaches to create new tandem repeat proteins. We propose to continue this work through two specific aims to further develop and improve upon computational approaches for protein design. As part of this project, we will solve atomic resolution crystal structures of many selected and designed molecular complexes and provide them to our immediate collaborators as well as to a public structure prediction project, for computational prediction challenges. Aim 1. We will design and characterize novel self-associating circular tandem repeat proteins (using both de novo computational design and using high-throughput selections) and then further design them to undergo ligand-induced protein-protein association. Beyond the challenge of combining protein scaffold design and ligand binding design, the motivation for this aim is to determine the structural and mechanistic features of small molecule ligand-binding, and balance of forces, that facilitate ligand-induced protein-protein association. Aim 2. We will improve our understanding and ability to design novel protein-DNA recognition specificities and behaviors. To accomplish this, we will: (1) Systematically select and optimize a series of variants of a model DNA-binding protein, that display altered binding specificity across two regions of partially overlapping sequential clusters of basepairs and neighboring protein residues. (2) Determine the high-resolution structures and binding behavior of each construct. (3) Supervise blinded computational efforts, using multiple approaches, to predict the same structures. (4) Compare and analyze the results of computational predictions versus multiple computational prediction strategies to define features influencing predictive accuracy. For both aims, we will further exploit our crystallographic structures by computationally ‘reverse engineering’ each construct using validated protein structures, to further understand the performance of design approaches.

项目总结

项目成果

De novo design of protein homodimers containing tunable symmetric protein pockets.

• DOI: 10.1073/pnas.2113400119
• 发表时间: 2022-07-26
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1

Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces.

• DOI: 10.1038/s42003-021-02766-y
• 发表时间: 2021-10-29
• 期刊: Communications biology
• 影响因子: 5.9
• 作者: Hallinan JP;Doyle LA;Shen BW;Gewe MM;Takushi B;Kennedy MA;Friend D;Roberts JM;Bradley P;Stoddard BL
• 通讯作者: Stoddard BL

Stepwise design of pseudosymmetric protein hetero-oligomers.

假对称蛋白质异源寡聚物的逐步设计。

• DOI: 10.1101/2023.04.07.535760
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Kibler,RyanD;Lee,Sangmin;Kennedy,MadisonA;Wicky,BasileIM;Lai,StellaM;Kostelic,MariusM;Li,Xinting;Chow,CameronM;Carter,Lauren;Wysocki,VickiH;Stoddard,BarryL;Baker,David
• 通讯作者: Baker,David

Immunization with a self-assembling nanoparticle vaccine displaying EBV gH/gL protects humanized mice against lethal viral challenge.

• DOI: 10.1016/j.xcrm.2022.100658
• 发表时间: 2022-06-21
• 期刊: CELL REPORTS MEDICINE
• 影响因子: 14.3
• 作者: Malhi, Harman;Homad, Leah J.;Wan, Yu-Hsin;Poudel, Bibhav;Fiala, Brooke;Borst, Andrew J.;Wang, Jing Yang;Walkey, Carl;Price, Jason;Wall, Abigail;Singh, Suruchi;Moodie, Zoe;Carter, Lauren;Handa, Simran;Correnti, Colin E.;Stoddard, Barry L.;Veesler, David;Pancera, Marie;Olson, James;King, Neil P.;McGuire, Andrew T.
• 通讯作者: McGuire, Andrew T.

De novo design of knotted tandem repeat proteins.

• DOI: 10.1038/s41467-023-42388-y
• 发表时间: 2023-10-24
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Doyle, Lindsey A.;Takushi, Brittany;Kibler, Ryan D.;Milles, Lukas F.;Orozco, Carolina T.;Jones, Jonathan D.;Jackson, Sophie E.;Stoddard, Barry L.;Bradley, Philip
• 通讯作者: Bradley, Philip