A theoretical view of the C3d:CR2 binding controversy

Mohan, Rohith R.; Gorham, Ronald D.; Morikis, Dimitrios

doi:10.1016/j.molimm.2014.11.006

Cited by 13 publications

(36 citation statements)

References 57 publications

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“…The reverse holds true as well where mutations of residues resulting in an increase in the association rate constant signify that the residue hinders the formation of the encounter complex. These results are in line with a previous computational alanine scan and electrostatic analysis study using AESOP 19 with a few small discrepancies such as K251A on C3d and R83A on CR2, which are close to the threshold of the error. Thus, we establish that the acceleration of the formation of the encounter complex due to electrostatic steering is affected by individual charged residues contributions as well.…”

Section: Resultssupporting

confidence: 92%

“…19 In particular, two clusters of C3d residues (D36, E37, and E39; E160, K162, D163, E166, and E167) demonstrate significant contributions to electrostatic interactions, intermolecular interaction occupancies (hydrogen bonds, salt bridges, and nonpolar interactions) and steered MD (SMD) simulations. The computational study also emphasizes the importance of both the SCR1 and SCR2 domain to the stability and energetics of the complex.…”

Section: Resultsmentioning

confidence: 99%

“…35,36,40−42 Although there was ambiguity and controversy for several years because of an older nonphysiological crystallographic structure of the C3d:CR2 complex, this controversy is now resolved with new crystallographic, mutagenesis and binding, and computational data. 19,36,41,43 A recent study has evaluated the physicochemical origins and strength of the C3d:CR2 interaction, using the physiological and the controversial crystallographic structures, and has demonstrated the electrostatic mechanism of binding. 19 This and earlier studies 37−39 have proposed a two-step model for C3d:CR2 association, consisting of recognition and binding for highly and oppositely charged proteins.…”

Section: Introductionmentioning

confidence: 99%

“…19,36,41,43 A recent study has evaluated the physicochemical origins and strength of the C3d:CR2 interaction, using the physiological and the controversial crystallographic structures, and has demonstrated the electrostatic mechanism of binding. 19 This and earlier studies 37−39 have proposed a two-step model for C3d:CR2 association, consisting of recognition and binding for highly and oppositely charged proteins. This model was based on earlier work on electrostatic steering in enzymatic reactions and protein interactions by McCammon and co-workers.…”

Section: Introductionmentioning

confidence: 99%

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Electrostatic Steering Accelerates C3d:CR2 Association

2016

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Electrostatic effects are ubiquitous in protein interactions and are found to be pervasive in the complement system as well. The interaction between complement fragment C3d and complement receptor 2 (CR2) has evolved to become a link between innate and adaptive immunity. Electrostatic interactions have been suggested to be the driving factor for the association of the C3d:CR2 complex. In this study, we investigate the effects of ionic strength and mutagenesis on the association of C3d:CR2 through Brownian dynamics simulations. We demonstrate that the formation of the C3d:CR2 complex is ionic strength-dependent, suggesting the presence of long-range electrostatic steering that accelerates the complex formation. Electrostatic steering occurs through the interaction of an acidic surface patch in C3d and the positively charged CR2 and is supported by the effects of mutations within the acidic patch of C3d that slow or diminish association. Our data are in agreement with previous experimental mutagenesis and binding studies and computational studies. Although the C3d acidic patch may be locally destabilizing because of unfavorable Coulombic interactions of like charges, it contributes to the acceleration of association. Therefore, acceleration of function through electrostatic steering takes precedence to stability. The site of interaction between C3d and CR2 has been the target for delivery of CR2-bound nanoparticle, antibody, and small molecule biomarkers, as well as potential therapeutics. A detailed knowledge of the physicochemical basis of C3d:CR2 association may be necessary to accelerate biomarker and drug discovery efforts.

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Section: Resultssupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Electrostatic Steering Accelerates C3d:CR2 Association

2016

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“…The alanine scan is a perturbation method of identifying individual amino acids that have a significant effect in the formation of the parent protein complex (loss of binding mutations). It can also identify mutations or sites of mutations that will enhance association (gain of binding mutations) in studies of design of protein-protein interfaces (29)(30)(31).…”

Section: Alanine Scan Mutagenesismentioning

confidence: 99%

AESOP: A Python Library for Investigating Electrostatics in Protein Interactions

Harrison

Mohan

Gorham

et al. 2017

Biophysical Journal

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Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion limited. To facilitate quantitative comparisons of electrostatics in protein families and to describe electrostatic contributions of individual amino acids, we previously developed a computational framework called AESOP. We now implement this computational tool in Python with increased usability and the capability of performing calculations in parallel. AESOP utilizes PDB2PQR and Adaptive Poisson-Boltzmann Solver to generate grid-based electrostatic potential files for protein structures provided by the end user. There are methods within AESOP for quantitatively comparing sets of grid-based electrostatic potentials in terms of similarity or generating ensembles of electrostatic potential files for a library of mutants to quantify the effects of perturbations in protein structure and protein-protein association.Electrostatics have been shown to play a pivotal role in guiding the association of a protein with its respective binding partner, forming the encounter complex (1-4). Additionally, electrostatic interactions can act to thermodynamically stabilize a protein complex (4). In attempts to improve protein activity, enhancing association rates is preferable to thermodynamic stabilization of the complex, as interactions are typically diffusion limited (1). To aid investigations into the electrostatics of protein interactions and to facilitate attempts to re-engineer protein behavior, our lab previously developed a computational tool for analysis of electrostatic structures of proteins (AESOP) (5-8). Here, we present an implementation of AESOP in Python (9) with increased functionality and the capability of parallel processing. This framework may be used to both compare electrostatic similarity of protein families and dissect the electrostatic contribution of individual amino acids to the free energy of association (5-8).Though several other computational tools have been developed for similar purposes, AESOP is the only platform, to our knowledge, that is focused on protein electrostatics and offers multiple computational methods for both family-based and single-structure-based analyses. In comparison, Surface Diver and PIPSA have been developed to compare electrostatic potentials across families of structurally homologous proteins. Surface Diver accomplishes this quantitative comparison without prior structural superpositioning through spherical harmonic decomposition (10), whereas PIPSA requires superpositioning and instead allows for comparisons between common structural regions that are functionally similar (11,12). Similar to PIPSA, AESOP requires superposed structures and quantitatively compares electrostatic potentials in a common grid space. PIPSA performs this comparison via calculation of a Hodgkin s...

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Energetic evaluation of binding modes in the C3d and Factor H (CCP 19‐20) complex

2015

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As a part of innate immunity, the complement system relies on activation of the alternative pathway (AP). While feed-forward amplification generates an immune response towards foreign surfaces, the process requires regulation to prevent an immune response on the surface of host cells. Factor H (FH) is a complement protein secreted by native cells to negatively regulate the AP. In terms of structure, FH is composed of 20 complement-control protein (CCP) modules that are structurally homologous but vary in composition and function. Mutations in these CCPs have been linked to states of autoimmunity. In particular, several mutations in CCP 19-20 are correlated to atypical hemolytic uremic syndrome (aHUS). From crystallographic structures there are three putative binding sites of CCP 19-20 on C3d. Since there has been some controversy over the primary mode of binding from experimental studies, we approach characterization of binding using computational methods. Specifically, we compare each binding mode in terms of electrostatic character, structural stability, dissociative and associative properties, and predicted free energy of binding. After a detailed investigation, we found two of the three binding sites to be similarly stable while varying in the number of contacts to C3d and in the energetic barrier to complex dissociation. These sites are likely physiologically relevant and may facilitate multivalent binding of FH CCP 19-20 to C3b and either C3d or host glycosaminoglycans. We propose thermodynamically stable binding with modules 19 and 20, the latter driven by electrostatics, acting synergistically to increase the apparent affinity of FH for host surfaces.Keywords: complement system; C3d; factor H; Poisson-Boltzmann electrostatics; molecular dynamics; steered molecular dynamics; MM/GBSA binding free energy Statement: Crystallographic structures propose three binding sites for the complex of immune system protein C3d with the regulator factor H 19-20. Since crystallization of proteins can perturb physiological protein structure, we computationally characterize the interactions at the three putative binding sites. Our studies contribute to understanding the physicochemical basis of FH 19-20 interactions with C3d and provide a molecular basis for understanding autoimmune diseases such as atypical hemolytic syndrome.Abbreviations: AP, alternative pathway; C3, complement component 3; C3b, complement component 3b; FB, factor B; C3a, complement component C3a; C3d, complement component 3d; FH, factor H; iC3b, proteolytically-inactive complement component 3b; CCP, complement control protein; aHUS, atypical hemolytic uremic syndrome; PDB, protein data bank; GAG, glycosaminoglycan; CR2, complement receptor 2; AESOP, analysis of electrostatic similarities of proteins; WT, wild type; MD, molecular dynamics; RMSD, root-mean-square deviation; SASA, solvent-accessible surface area; SMD, steered molecular dynamics; MM/GBSA, molecular mechanics/generalized Born surface area.Additional Supporting Information may be fo...

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A theoretical view of the C3d:CR2 binding controversy

Cited by 13 publications

References 57 publications

Electrostatic Steering Accelerates C3d:CR2 Association

Electrostatic Steering Accelerates C3d:CR2 Association

AESOP: A Python Library for Investigating Electrostatics in Protein Interactions

Energetic evaluation of binding modes in the C3d and Factor H (CCP 19‐20) complex

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