INTERACTION DESIGN · De novo design of affinity, specificity, and multispecificity in synthetic protein interaction networks
FP7 — People (Marie Curie Actions)
- Duration
- 2012-08-01 → 2016-07-31
- EU contribution
- €100,000
- Participants
- 1
- Scheme
- MC-CIG
Lines connect the coordinator with its partners.
Results in brief
De novo design of affinity, specificity, and multispecificity in synthetic protein interaction networks
Proteins are central to all life processes. The ability to design new or improved functions in proteins therefore holds the promise of control over the most fundamental aspects that determine health and disease. Our laboratory develops computer algorithms and experimental methods for designing new functions in proteins. During the course of the project we have developed new methods for designing immune-system antibodies to target desired molecules and methods to engineer novel molecular specificities in protein interaction networks. Recently, we extended these methods to also design novel enzymes to catalyze desired chemical transformations. To achieve these goals, we have used iterative cycles of algorithm development and experimental testing. During the course of these cycles we have seen that the stability of designed proteins improves drastically from cycle to cycle, and we have shown that some of the lessons we have learned from designing novel proteins can be extended to ill-behaved natural proteins to drastically improve their stability. Our design algorithm is general and fully automated, and can be accessed through a webserver. We have shown that the algorithm can be used to improve the stability of therapeutic antibodies, enzymes for industrial processes, and vaccine components. Our work has therefore extended the reach of design of function to areas that can make substantial contributions to research, biotechnology, and public health.
Data: CORDIS, © European Union
Project objective
The two most fundamental features of molecular recognition are affinity and specificity. The proposed research aims to develop a new methodology for de novo design of small interaction networks not seen in Nature and to generate such networks with predetermined levels of specificity and affinity. In Preliminary Results we developed a methodology to de novo design protein binders of surfaces that have not been structurally characterized in bound form. We used this method to design three experimentally validated medium-affinity binders of the apo form of an acyl carrier protein (ACP), which has no co-crystal structures, demonstrating that interaction design could target a broad range of physicochemically appropriate surfaces. This synthetic network is the first multispecific system (one ACP interacts with three unrelated proteins), which is completely devoid of selective pressures for function other than binding, and will serve as a model to study how high affinity, specificity, and multispecificity might arise from non-interacting proteins. We will develop a multidisciplinary computational/experimental approach to substantially increase the affinity of the ACP to its binders by introducing stabilizing substitutions to residues on either one or both sides of each designed interface. Affinity will be further increased by experimental in vitro selection of higher-affinity variants of the ACP or of its partners. We will additionally erect specificity barriers between the ACP-binder pairs by redesigning the amino acid identities and backbones of interfacial loops. Specificity and affinity are important features in many protein-engineering applications, including the development of protein therapeutics and diagnostics, and the generation of synthetic signaling and metabolic networks. Small networks, such as the ones we produce here, may be future building blocks in these applications.
Original text from CORDIS.
Participants
- WEIZMANN INSTITUTE OF SCIENCE · RehovotCoordinatorIsrael
Links
Data: CORDIS, © European Union