Computational Redesign of a Protein–Protein Interface for High Affinity and Binding Specificity Using Modular Architecture and Naturally Occurring Template Fragments

Potapov, Vladimir; Reichmann, Dana; Abramovich, Renne; Filchtinski, Daniel; Zohar, Nir; Halevy, Daniel Ben; Edelman, Marvin; Sobolev, V. M.; Schreiber, Gideon

doi:10.1016/j.jmb.2008.08.078

Cited by 44 publications

(33 citation statements)

References 36 publications

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“…1) (27,28). Previously, we used cluster analysis to computationally compare these interfaces (27,40). The cluster analysis allowed for the identification of BLIP-II residues that formed H-bonds, electrostatic interactions, van der Waals contacts, and/or noncanonical interactions (such as cation-) with ␤-lactamase.…”

Section: Resultsmentioning

confidence: 99%

Identification of the β-Lactamase Inhibitor Protein-II (BLIP-II) Interface Residues Essential for Binding Affinity and Specificity for Class A β-Lactamases

Brown¹,

Chow²,

Ruprecht³

et al. 2013

Journal of Biological Chemistry

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Section: Resultsmentioning

confidence: 99%

Identification of the β-Lactamase Inhibitor Protein-II (BLIP-II) Interface Residues Essential for Binding Affinity and Specificity for Class A β-Lactamases

Brown¹,

Chow²,

Ruprecht³

et al. 2013

Journal of Biological Chemistry

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“…3,4 Nevertheless, major advances have been reported in the de novo design of PPIs, as well as in the redesign of naturally occurring complex specificity, in many instances incorporating negative design to enhance selectivity. [4][5][6][7][8][9][10] The power of such approaches was shown by Fleishman et al in their recent de novo design of proteins targeting the conserved stem region of influenza hemagglutinin, with the resulting binary complex structures closely matching those designed computationally. 11 The strategy adopted in this case involved computing important amino acid hotspot residues onto a guest scaffold and then optimizing shape complementarity and affinity from which high-affinity binders were isolated.…”

Section: Introductionmentioning

confidence: 99%

Structure of the Ultra-High-Affinity Colicin E2 DNase–Im2 Complex

Wojdyla¹,

Fleishman²,

Baker³

et al. 2012

Journal of Molecular Biology

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“…More recently, computational (re)design (13 and 14) and directed evolution experiments (15 and 16) have been developed. The former provides a useful yardstick for gauging how well PPI specificity is understood; currently, the largest changes in specificity that have been designed into an interface are of the order of 10 2 -to 10 3 -fold (17)(18)(19)(20). While this represents significant progress, when set against the >10 10 -fold range of binding affinities that PPIs can exhibit in nature (21) it highlights how much remains to be uncovered.…”

mentioning

confidence: 99%

The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

Meenan

Sharma

Fleishman

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

113

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High-affinity, high-selectivity protein-protein interactions that are critical for cell survival present an evolutionary paradox: How does selectivity evolve when acquired mutations risk a lethal loss of high-affinity binding? A detailed understanding of selectivity in such complexes requires structural information on weak, noncognate complexes which can be difficult to obtain due to their transient and dynamic nature. Using NMR-based docking as a guide, we deployed a disulfide-trapping strategy on a noncognate complex between the colicin E9 endonuclease (E9 DNase) and immunity protein 2 (Im2), which is seven orders of magnitude weaker binding than the cognate femtomolar E9 DNase-Im9 interaction. The 1.77 Å crystal structure of the E9 DNase-Im2 complex reveals an entirely noncovalent interface where the intersubunit disulfide merely supports the crystal lattice. In combination with computational alanine scanning of interfacial residues, the structure reveals that the driving force for binding is so strong that a severely unfavorable specificity contact is tolerated at the interface and as a result the complex becomes weakened through "frustration." As well as rationalizing past mutational and thermodynamic data, comparing our noncognate structure with previous cognate complexes highlights the importance of loop regions in developing selectivity and accentuates the multiple roles of buried water molecules that stabilize, ameliorate, or aggravate interfacial contacts. The study provides direct support for dual-recognition in colicin DNase-Im protein complexes and shows that weakened noncognate complexes are primed for high-affinity binding, which can be achieved by economical mutation of a limited number of residues at the interface.colicins | crystallography | disulfide-trapping | specificity | frustration S pecificity in protein-protein interactions (PPIs) is critical for the organization of macromolecular complexes involved in all aspects of cellular homeostasis and differentiation. Within the vast interaction networks in cells there is significant redundancy, with many proteins acting as "hubs" that recognize multiple binding partners (1), and yet also significant discrimination (2). The factors that tip the balance in favor of specificity or promiscuity in PPIs while not clear are coming under increasing scrutiny (3). Understanding this balance is critical both from fundamental and applied perspectives. Protein therapeutics are finding increasing use in medicine but off-target effects can have disastrous consequences (4). High-affinity, high-selectivity binding is therefore an essential goal in such engineered platforms. Advances in defining the molecular and thermodynamic basis for binding affinity have been made in a multitude of natural and engineered/designed PPIs (5-7), but our molecular knowledge of specificity remains rudimentary. In large part this is due to the lack of highresolution structural information on weak and transient proteinprotein complexes that are evolutionarily related to a cognate hig...

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Computational Redesign of a Protein–Protein Interface for High Affinity and Binding Specificity Using Modular Architecture and Naturally Occurring Template Fragments

Cited by 44 publications

References 36 publications

Identification of the β-Lactamase Inhibitor Protein-II (BLIP-II) Interface Residues Essential for Binding Affinity and Specificity for Class A β-Lactamases

Identification of the β-Lactamase Inhibitor Protein-II (BLIP-II) Interface Residues Essential for Binding Affinity and Specificity for Class A β-Lactamases

Structure of the Ultra-High-Affinity Colicin E2 DNase–Im2 Complex

The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

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