Relative solvent accessible surface area predicts protein conformational changes upon binding

Protein interactions are often accompanied by significant changes in conformation. We have analyzed the relationships between protein structures and the conformational changes they undergo upon binding. Based upon this, we introduce a simple measure, the relative solvent accessible surface area, which can be used to predict the magnitude of binding-induced conformational changes from the structures of either monomeric proteins or bound subunits. Applying this to a large set of protein complexes suggests that large conformational changes upon binding are common. In addition, we observe considerable enrichment of intrinsically disordered sequences in proteins predicted to undergo large conformational changes. Finally, we demonstrate that the relative solvent accessible surface area of monomeric proteins can be used as a simple proxy for protein flexibility. This reveals a powerful connection between the flexibility of unbound proteins and their binding-induced conformational changes, consistent with the conformational selection model of molecular recognition.     

Evaluating conformational changes in protein structures binding RNA

Many protein-RNA recognition events are known to exhibit conformational changes from qualitative observations of individual complexes. However, a quantitative estimation of conformational changes is required if protein-RNA docking and template-based methods for RNA binding site prediction are to be developed. This study presents the first quantitative evaluation of conformational changes that occur when proteins bind RNA. The analysis of twelve RNA-binding proteins in the bound and unbound states using error-scaled difference distance matrices is presented. The binding site residues are mapped to each structure, and the conformational changes that affect these residues are evaluated. Of the twelve proteins four exhibit greater movements in nonbinding site residues, and a further four show the greatest movements in binding site residues. The remaining four proteins display no significant conformational change. When interface residues are found to be in conformationally variable regions of the protein they are typically seen to move less than 2 A between the bound and unbound conformations. The current data indicate that conformational changes in the binding site residues of RNA binding proteins may not be as significant as previously suggested, but a larger data set is required before wider conclusions may be drawn. The implications of the observed conformational changes for protein function prediction are discussed.     

Conformational changes in DNA‐binding proteins: Relationships with precomplex features and contributions to specificity and stability

Both Proteins and DNA undergo conformational changes in order to form functional complexes and also to facilitate interactions with other molecules. These changes have direct implications for the stability and specificity of the complex, as well as the cooperativity of interactions between multiple entities. In this work, we have extensively analyzed conformational changes in DNA‐binding proteins by superimposing DNA‐bound and unbound pairs of protein structures in a curated database of 90 proteins. We manually examined each of these pairs, unified the authors' annotations, and summarized our observations by classifying conformational changes into six structural categories. We explored a relationship between conformational changes and functional classes, binding motifs, target specificity, biophysical features of unbound proteins, and stability of the complex. In addition, we have also investigated the degree to which the intrinsic flexibility can explain conformational changes in a subset of 52 proteins with high quality coordinate data. Our results indicate that conformational changes in DNA‐binding proteins contribute significantly to both the stability of the complex and the specificity of targets recognized by them. We also conclude that most conformational changes occur in proteins interacting with specific DNA targets, even though unbound protein structures may have sufficient information to interact with DNA in a nonspecific manner. Proteins 2014; 82:841–857. © 2013 Wiley Periodicals, Inc.     

A model of threshold behavior reveals rescue mechanisms of bystander proteins in conformational diseases

Conformational diseases result from the failure of a specific protein to fold into its correct functional state. The misfolded proteins can lead to the toxic aggregation of proteins. Protein misfolding in conformational diseases often displays a threshold behavior characterized by a sudden shift between nontoxic to toxic levels of misfolded proteins. In some conformational diseases, evidence suggests that misfolded proteins interact with bystander proteins (unfolded and native folded proteins), eliciting a misfolded phenotype. These bystander isomers would follow their normal physiological pathways in absence of misfolded proteins. In this article, we present a general mechanism of bystander and misfolded protein interaction which we have used to investigate how the threshold behavior in protein misfolding is triggered in conformational diseases. Using a continuous flow reactor model of the endoplasmic reticulum, we found that slight changes in the bystander protein residence time in the endoplasmic reticulum or the ratio of basal misfolded to bystander protein inflow rates can trigger the threshold behavior in protein misfolding. Our analysis reveals three mechanisms to rescue bystander proteins in conformational diseases. The results of our model can now help direct experiments to understand the threshold behavior and develop therapeutic strategies targeting the modulation of conformational diseases.     

What the protein data bank tells us about the evolutionary conservation of protein conformational diversity

Proteins sample a multitude of different conformations by undergoing small‐ and large‐scale conformational changes that are often intrinsic to their functions. Information about these changes is often captured in the Protein Data Bank by the apparently redundant deposition of independent structural solutions of identical proteins. Here, we mine these data to examine the conservation of large‐scale conformational changes between homologous proteins. This is important for both practical reasons, such as predicting alternative conformations of a protein by comparative modeling, and conceptual reasons, such as understanding the extent of conservation of different features in evolution. To study this question, we introduce a novel approach to compare conformational changes between proteins by the comparison of their difference distance maps (DDMs). We found that proteins undergoing similar conformational changes have similar DDMs and that this similarity could be quantified by the correlation between the DDMs. By comparing the DDMs of homologous protein pairs, we found that large‐scale conformational changes show a high level of conservation across a broad range of sequence identities. This shows that conformational space is usually conserved between homologs, even relatively distant ones.     

Probing the activation-promoted structural rearrangements in preassembled receptor-G protein complexes

Activation of heterotrimeric G proteins by their cognate seven transmembrane domain receptors is believed to involve conformational changes propagated from the receptor to the G proteins. However, the nature of these changes remains unknown. We monitored the conformational rearrangements at the interfaces between receptors and G proteins and between G protein subunits by measuring bioluminescence resonance energy transfer between probes inserted at multiple sites in receptor-G protein complexes. Using the data obtained for the alpha(2A)AR-G alpha(i1) beta1gamma2 complex and the available crystal structures of G alpha(i1) beta1gamma2, we propose a model wherein agonist binding induces conformational reorganization of a preexisting receptor-G protein complex, leading the G alpha-G betagamma interface to open but not dissociate. This conformational change may represent the movement required to allow nucleotide exit from the G alpha subunit, thus reflecting the initial activation event.     

Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis

The conformational change of a protein upon ligand binding was examined by normal mode analysis (NMA) based on an elastic-network model (ENM) for a full-atom system using dihedral angles as independent variables. Specifically, we investigated the extent to which conformational change vectors of atoms from an apo form to a holo form of a protein can be represented by a linear combination of the displacement vectors of atoms in the apo form calculated for the lowest-frequency m normal modes (m=1, 2,…, 20). In this analysis, the latter vectors were best fitted to the former ones by the least-squares method. Twenty-two paired proteins in the holo and apo forms, including three dimer pairs, were examined. The results showed that, in most cases, the conformational change vectors were reproduced well by a linear combination of the displacement vectors of a small number of low-frequency normal modes. The conformational change around an active site was reproduced as well as the entire conformational change, except for some proteins that only undergo significant conformational changes around active sites. The weighting factors for 20 normal modes optimized by the least-squares fitting characterize the conformational changes upon ligand binding for these proteins. The conformational changes sampled around the apo form of a protein by the linear combination of the displacement vectors obtained by ENM-based NMA may help solve the flexible-docking problem of a protein with another molecule because the results presented herein suggest that they have a relatively high probability of being involved in an actual conformational change.     

Protein Conformational Changes Are Detected and Resolved Site Specifically by Second-Harmonic Generation

We present here a straightforward, broadly applicable technique for real-time detection and measurement of protein conformational changes in solution. This method is based on tethering proteins labeled with a second-harmonic generation (SHG) active dye to supported lipid bilayers. We demonstrate our method by measuring the conformational changes that occur upon ligand binding with three well-characterized proteins labeled at lysine residues: calmodulin (CaM), maltose-binding protein (MBP), and dihydrofolate reductase (DHFR). We also create a single-site cysteine mutant of DHFR engineered within the Met20 catalytic loop region and study the protein’s structural motion at this site. Using published x-ray crystal structures, we show that the changes in the SHG signals upon ligand binding are the result of structural motions that occur at the labeled sites between the apo and ligand-bound forms of the proteins, which are easily distinguished from each other. In addition, we demonstrate that different magnitudes of the SHG signal changes are due to different and specific ligand-induced conformational changes. Taken together, these data illustrate the potential of the SHG approach for detecting and measuring protein conformational changes for a wide range of biological applications.     

A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks

The study of protein binding mechanisms is a major topic of research in structural biology. Here, we implement a combination of metrics to systematically assess the cost of backbone conformational changes that protein domains undergo upon association. Through the analyses of 2090 unique unbound → bound transitions, from over 12,000 structures, we show that two-thirds of these proteins do not suffer significant structural changes upon binding, and could thus fit the lock-and-key model well. Among the remaining proteins, one-third explores the bound conformation in the unbound state (conformational selection model) and, while most transitions are possible from an energetic perspective, a few do require external help to break the thermodynamic barrier (induced fit model). We also analyze the relationship between conformational transitions and protein connectivity, finding that, in general, domains interacting with many partners undergo smaller changes upon association, and are less likely to freely explore larger conformational changes.