Hot Spot Occlusion from Bulk Water: a Comprehensive Study of the Complex between the Lysozyme HEL and the Antibody FVD1.3

Residue-level determinants of angiopoietin-2 interactions with its receptor Tie2

We combined computational and experimental methods to interrogate the binding determinants of angiopoietin-2 (Ang2) to its receptor tyrosine kinase (RTK) Tie2-a central signaling system in angiogenesis, inflammation, and tumorigenesis. We used physics-based electrostatic and surface-area calculations to identify the subset of interfacial Ang2 and Tie2 residues that can affect binding directly. Using random and site-directed mutagenesis and yeast surface display (YSD), we validated these predictions and identified additional Ang2 positions that affected receptor binding. We then used burial-based calculations to classify the larger set of Ang2 residues that are buried in the Ang2 core, whose mutations can perturb the Ang2 structure and thereby affect interactions with Tie2 indirectly. Our analysis showed that the Ang2-Tie2 interface is dominated by nonpolar contributions, with only three Ang2 and two Tie2 residues that contribute electrostatically to intermolecular interactions. Individual interfacial residues contributed only moderately to binding, suggesting that engineering of this interface will require multiple mutations to reach major effects. Conversely, substitutions in substantially buried Ang2 residues were more prevalent in our experimental screen, reduced binding substantially, and are therefore more likely to have a deleterious effect that might contribute to oncogenesis. Computational analysis of additional RTK-ligand complexes, c-Kit-SCF and M-CSF-c-FMS, and comparison to previous YSD results, further show the utility of our combined methodology.

A polar ring endows improved specificity to an antibody fragment

Engineering monovalent Fab fragments into bivalent formats like IgGs or F(ab')2 can lead to aggregation presumably because of nonspecific off-target interactions that induce aggregation. In an effort to further understand the molecular determinants of nonspecific interactions for engineered antibodies and natively folded proteins in general, we focused on a synthetic Fab with low nanomolar affinity to histone chaperone Anti-silencing factor 1 (Asf1) that demonstrates off-target binding through low solubility (∼5 mg/mL) in the multivalent F(ab') 2 state. Here, we generated phage display-based shotgun scanning libraries to introduce aspartate as a negative design element into the antibody paratope. The antibody-combining site was amenable to aspartate substitution at numerous positions within the antigen binding loops and one variant, Tyr(L93) Asp/His(L94) Asp/Thr(H100b) Asp, possessed high solubility (>100 mg/ml). Furthermore, the mutations decreased nonspecific interactions measured by column interaction chromatography and ELISA in the multivalent antibody format while maintaining high affinity to the antigen. Structural determination of the antibody-antigen complex revealed that the aspartate-permissive residues formed a polar ring around the structural and functional paratope, recapitulating the canonical feature of naturally occurring protein-protein interactions. This observation may inform future strategies for the design and engineering of molecular recognition.

Antibody Binding Selectivity: Alternative Sets of Antigen Residues Entail High-Affinity Recognition

Understanding the relationship between protein sequence and molecular recognition selectivity remains a major challenge. The antibody fragment scFv1F4 recognizes with sub nM affinity a decapeptide (sequence 6TAMFQDPQER15) derived from the N-terminal end of human papilloma virus E6 oncoprotein. Using this decapeptide as antigen, we had previously shown that only the wild type amino-acid or conservative replacements were allowed at positions 9 to 12 and 15 of the peptide, indicating a strong binding selectivity. Nevertheless phenylalanine (F) was equally well tolerated as the wild type glutamine (Q) at position 13, while all other amino acids led to weaker scFv binding. The interfaces of complexes involving either Q or F are expected to diverge, due to the different physico-chemistry of these residues. This would imply that high-affinity binding can be achieved through distinct interfacial geometries. In order to investigate this point, we disrupted the scFv-peptide interface by modifying one or several peptide positions. We then analyzed the effect on binding of amino acid changes at the remaining positions, an altered susceptibility being indicative of an altered role in complex formation. The 23 starting variants analyzed contained replacements whose effects on scFv1F4 binding ranged from minor to drastic. A permutation analysis (effect of replacing each peptide position by all other amino acids except cysteine) was carried out on the 23 variants using the PEPperCHIP® Platform technology. A comparison of their permutation patterns with that of the wild type peptide indicated that starting replacements at position 11, 12 or 13 modified the tolerance to amino-acid changes at the other two positions. The interdependence between the three positions was confirmed by SPR (Biacore® technology). Our data demonstrate that binding selectivity does not preclude the existence of alternative high-affinity recognition modes.

What Glues a Homodimer Together: Systematic Analysis of the Stabilizing Effect of an Aromatic Hot Spot in the Protein-Protein Interface of the tRNA-Modifying Enzyme Tgt

Shigella bacteria constitute the causative agent of bacillary dysentery, an acute inflammatory disease causing the death of more than one million humans per year. A null mutation in the tgt gene encoding the tRNA-modifying enzyme tRNA-guanine transglycosylase (Tgt) was found to drastically decrease the pathogenicity of Shigella bacteria, suggesting the use of Tgt as putative target for selective antibiotics. The enzyme is only functionally active as a homodimer; thus, interference with the formation of its protein-protein interface is an attractive opportunity for therapeutic intervention. To better understand the driving forces responsible for the assembly, stability, and formation of the homodimer, we studied the properties of the residues that establish the dimer interface in detail. We performed site-directed mutagenesis and controlled shifts in the monomer/dimer equilibrium ratio in solution in a concentration-dependent manner by native mass spectrometry and used crystal structure analysis to elucidate the geometrical modulations resulting from mutational variations. The wild-type enzyme exhibits nearly exclusive dimer geometry. A patch of four aromatic amino acids, embedded into a ring of hydrophobic residues and further stabilized by a network of H-bonds, is essential for the stability of the dimer's contact. Accordingly, any perturbance in the constitution of this aromatic patch by nonaromatic residues reduces dimer stability significantly, with some of these exchanges resulting in a nearly exclusively monomeric state. Apart from the aromatic hot spot, the interface comprises an extended loop-helix motif that exhibits remarkable flexibility. In the destabilized mutated variants, the loop-helix motif adopts deviating conformations in the interface region, and a number of water molecules, penetrating into the interface, are observed.

A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy

Protein-protein (P-P) 3D structures are fundamental to structural biology and drug discovery. However, most of them have never been determined. Many docking algorithms were developed for that purpose, but they have a very limited accuracy in generating native-like structures and identifying the most correct one, in particular when a single answer is asked for. With such a low success rate it is difficult to point out one docked structure as being native-like. Here we present a new, high accuracy, scoring method to identify the 3D structure of P-P complexes among a set of trial poses. It incorporates alanine scanning mutagenesis experimental data that need to be obtained a priori. The scoring scheme works by matching the computational and the experimental alanine scanning mutagenesis results. The size of the trial P-P interface area is also taken into account. We show that the method ranks the trial structures and identifies the native-like structures with unprecedented accuracy (∼94%), providing the correct P-P 3D structures that biochemists and molecular biologists need to pursue their studies. With such a success rate, the bottleneck of protein-protein docking moves from the scoring to searching algorithms.

Hot spot-based design of small-molecule inhibitors for protein-protein interactions

Protein-protein interactions (PPIs) are important targets for the development of chemical probes and therapeutic agents. From the initial discovery of the existence of hot spots at PPI interfaces, it has been proposed that hot spots might provide the key for developing small-molecule PPI inhibitors. However, there has been no review on the ways in which the knowledge of hot spots can be used to achieve inhibitor design, nor critical examination of successful examples. This Digest discusses the characteristics of hot spots and the identification of druggable hot spot pockets. An analysis of four examples of hot spot-based design reveals the importance of this strategy in discovering potent and selective PPI inhibitors. A general procedure for hot spot-based design of PPI inhibitors is outlined.

Solvent-accessible surface area: How well can be applied to hot-spot detection?

A detailed comprehension of protein-based interfaces is essential for the rational drug development. One of the key features of these interfaces is their solvent accessible surface area profile. With that in mind, we tested a group of 12 SASA-based features for their ability to correlate and differentiate hot- and null-spots. These were tested in three different data sets, explicit water MD, implicit water MD, and static PDB structure. We found no discernible improvement with the use of more comprehensive data sets obtained from molecular dynamics. The features tested were shown to be capable of discerning between hot- and null-spots, while presenting low correlations. Residue standardization such as rel SASAi or rel/res SASAi , improved the features as a tool to predict ΔΔGbinding values. A new method using support machine learning algorithms was developed: SBHD (Sasa-Based Hot-spot Detection). This method presents a precision, recall, and F1 score of 0.72, 0.81, and 0.76 for the training set and 0.91, 0.73, and 0.81 for an independent test set.

Computational Alanine Scanning Mutagenesis-An Improved Methodological Approach for Protein-DNA Complexes

Proteins and protein-based complexes are the basis of many key systems in nature and have been the subject of intense research in the last decades, in an attempt to acquire comprehensive knowledge of reactions that take place in nature. Computational Alanine Scanning Mutagenesis approaches have been extensively used in the study of protein interfaces and in the determination of the most important residues for complex formation, the Hot-spots. However, as it is usually applied to the study of protein-protein interfaces, we tried to modify and apply it to the study of protein-DNA interfaces, which are also crucial in nature but have not been the subject of as much research. In this work, we carry out MD simulations of seven protein-DNA complexes and tested the influence of the variation of different parameters on the determination of the binding free energy terms (ΔΔGbinding) of 78 mutations: solvent representation, internal dielectric constant, Linear and Nonlinear Poisson-Boltzmann equation, Generalized Born model, simulation time, number of structures analyzed, number of MD trajectories, force field used, and energetic terms involved. Overall, this new approach gave an average error of 1.55 kcal/mol, and P, R, F1, accuracy, and specificity values of 0.78, 0.50, 0.61, 0.77, and 0.92, respectively. This improved computational alanine scanning mutagenesis approach may serve as a tool to explore the behavior of this important class of complexes.

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI

Understanding protein-protein association and being able to determine the crucial residues responsible for their association (hot-spots) is a key issue with huge practical applications such as rational drug design and protein engineering. A variety of computational methods exist to detect hot-spots residues, but the development of a fast and accurate quantitative alanine scanning mutagenesis (ASM) continues to be crucial. Using four protein-protein complexes, we have compared a variation of the standard computational ASM protocol developed at our group, based on the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) approach, against Thermodynamic Integration (TI), a well-known and accurate but computationally expensive method. To compare the efficiency and the accuracy of the two methods, we have calculated the protein-protein binding free energy differences upon alanine mutation of interfacial residues (ΔΔGbind). In relation to the experimental ΔΔGbind values, the average error obtained with TI was 1.53 kcal/mol, while the ASM protocol resulted in an average error of 1.18 kcal/mol. The results demonstrate that the much faster ASM protocol gives results at the same level of accuracy as the TI method but at a fraction of the computational time required to run TI. This ASM protocol is therefore a strong and efficient alternative to the systematic evaluation of protein-protein interfaces, involving hundreds of amino acid residues in search of hot-spots.

A negative feedback loop that limits the ectopic activation of a cell type-specific sporulation sigma factor of Bacillus subtilis

Two highly similar RNA polymerase sigma subunits, σ^F and σ^G, govern the early and late phases of forespore-specific gene expression during spore differentiation in Bacillus subtilis. σ^F drives synthesis of σ^G but the latter only becomes active once engulfment of the forespore by the mother cell is completed, its levels rising quickly due to a positive feedback loop. The mechanisms that prevent premature or ectopic activation of σ^G while discriminating between σ^F and σ^G in the forespore are not fully comprehended. Here, we report that the substitution of an asparagine by a glutamic acid at position 45 of σ^G (N45E) strongly reduced binding by a previously characterized anti-sigma factor, CsfB (also known as Gin), in vitro, and increased the activity of σ^G in vivo. The N45E mutation caused the appearance of a sub-population of pre-divisional cells with strong activity of σ^G. CsfB is normally produced in the forespore, under σ^F control, but sigGN45E mutant cells also expressed csfB and did so in a σ^G-dependent manner, autonomously from σ^F. Thus, a negative feedback loop involving CsfB counteracts the positive feedback loop resulting from ectopic σ^G activity. N45 is invariant in the homologous position of σ^G orthologues, whereas its functional equivalent in σ^F proteins, E39, is highly conserved. While CsfB does not bind to wild-type σ^F, a E39N substitution in σ^F resulted in efficient binding of CsfB to σ^F. Moreover, under certain conditions, the E39N alteration strongly restrains the activity of σ^F in vivo, in a csfB-dependent manner, and the efficiency of sporulation. Therefore, a single amino residue, N45/E39, is sufficient for the ability of CsfB to discriminate between the two forespore-specific sigma factors in B. subtilis.

Positive auto-regulation of a transcriptional activator during cell differentiation or development often allows the rapid and robust deployment of cell- and stage-specific genes and the routing of the differentiating cell down a specific path. Positive auto-regulation however, raises the potential for inappropriate activity of the transcription factor. Here we unravel the role of a previously characterized anti-sigma factor, CsfB, in a negative feedback loop that prevents ectopic expression of the sporulation-specific sigma factor σ^G of Bacillus subtilis. σ^G is activated in the forespore, one of the two chambers of the developing cell, at an intermediate stage in spore development. Once active, a positive feedback loop allows the rapid accumulation of σ^G. Synthesis of both σ^G and CsfB is under the control of the early forespore regulator σ^F, and CsfB may help prevent the premature activity of σ^G in the forespore. However, CsfB is also produced under σ^G control in non-sporulating cells, setting a negative feedback loop that we show limits its ectopic activation. We further show that an asparagine residue conserved among σ^G orthologues is critical for binding and inhibition by CsfB, whereas the exclusion of asparagine from the homologous position in σ^F confers immunity to CsfB.

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

The unanimous agreement that cellular processes are (largely) governed by interactions between proteins has led to enormous community efforts culminating in overwhelming information relating to these proteins; to the regulation of their interactions, to the way in which they interact and to the function which is determined by these interactions. These data have been organized in databases and servers. However, to make these really useful, it is essential not only to be aware of these, but in particular to have a working knowledge of which tools to use for a given problem; what are the tool advantages and drawbacks; and no less important how to combine these for a particular goal since usually it is not one tool, but some combination of tool-modules that is needed. This is the goal of this review.

Hot spots-A review of the protein-protein interface determinant amino-acid residues

Proteins tendency to bind to one another in a highly specific manner forming stable complexes is fundamental to all biological processes. A better understanding of complex formation has many practical applications, which include the rational design of new therapeutic agents, and the analysis of metabolic and signal transduction networks. Alanine-scanning mutagenesis made possible the detection of the functional epitopes, and demonstrated that most of the protein-protein binding energy is related only to a group of few amino acids at intermolecular protein interfaces: the hot spots. The scope of this review is to summarize all the available information regarding hot spots for a better atomic understanding of their structure and function. The ultimate objective is to improve the rational design of complexes of high affinity and specificity as well as that of small molecules, which can mimic the functional epitopes of the proteic complexes.