Intramolecular Binding Research Articles

Substrate Binding Switches the Conformation at the Lynchpin Site in the Substrate-Binding Domain of Human Hsp70 to Enable Allosteric Interdomain Communication.

The stress-induced 70 kDa heat shock protein (Hsp70) functions as a molecular chaperone to maintain protein homeostasis. Hsp70 contains an N-terminal ATPase domain (NBD) and a C-terminal substrate-binding domain (SBD). The SBD is divided into the β subdomain containing the substrate-binding site (βSBD) and the α-helical subdomain (αLid) that covers the βSBD. In this report, the solution structures of two different forms of the SBD from human Hsp70 were solved. One structure shows the αLid bound to the substrate-binding site intramolecularly, whereas this intramolecular binding mode is absent in the other structure solved. Structural comparison of the two SBDs from Hsp70 revealed that client-peptide binding rearranges residues at the interdomain contact site, which impairs interdomain contact between the SBD and the NBD. Peptide binding also disrupted the inter-subdomain interaction connecting the αLid to the βSBD, which allows the binding of the αLid to the NBD. The results provide a mechanism for interdomain communication upon substrate binding from the SBD to the NBD via the lynchpin site in the βSBD of human Hsp70. In comparison to the bacterial ortholog, DnaK, some remarkable differences in the allosteric signal propagation among residues within the Hsp70 SBD exist.

Chiral Cu(ii), Co(ii) and Ni(ii) complexes based on 2,2'-bipyridine modified peptoids.

Helical peptoids bearing 2,2'-bipyridine, varied in their chiral bulky side chains and their N-terminus form complexes with Cu(ii), Co(ii) and Ni(ii) via intramolecular binding. Chiral induction from the peptoid to each metal center could be only observed in some cases and is dependent on the identity of the N-terminus and on its position relative to the metal center.

Sterol Oxidation Mediates Stress-Responsive Vms1 Translocation to Mitochondria

Vms1 translocates to damaged mitochondria in response to stress, whereupon its binding partner, Cdc48, contributes to mitochondrial protein homeostasis. Mitochondrial targeting of Vms1 is mediated by its conserved mitochondrial targeting domain (MTD), which, in unstressed conditions, is inhibited by intramolecular binding to the Vms1 leucine-rich sequence (LRS). Here, we report a 2.7Å crystal structure of Vms1 that reveals that the LRS lies in a hydrophobic groove in the autoinhibited MTD. We also demonstrate that the oxidized sterol, ergosterol peroxide, is necessary and sufficient for Vms1 localization to mitochondria, through binding the MTD in an interaction that is competitive with binding to the LRS. These data support a model in which stressed mitochondria generate an oxidized sterol receptor that recruits Vms1 to support mitochondrial protein homeostasis.

Single Chain Polymeric Nanoparticles to Promote Selective Hydroxylation Reactions of Phenol Catalyzed by Copper.

Metal-containing single chain polymeric nanoparticles (SCPNs) can be used as synthetic mimics of metalloenzymes. Currently, the role of the folded polymer backbones on the activity and selectivity of metal sites is not clear. Herein, we report our findings on how polymeric frameworks modulate the coordination of Cu sites and the catalytic activity/selectivity of Cu-containing SCPNs mimicking monophenol hydroxylation reactions. Imidazole-functionalized copolymers of poly(methyl methacrylate-co-3-imidazolyl-2-hydroxy propyl methacrylate) were used for intramolecular Cu-imidazole binding that triggered the self-folding of polymers. Polymer chains imposed steric hindrance which yielded unsaturated Cu sites with an average coordination number of 3.3. Cu-containing SCPNs showed a high selectivity for the hydroxylation reaction of phenol to catechol, >80%, with a turnover frequency of >870 h-1 at 60 °C. The selectivity was largely influenced by the flexibility of the folded polymer backbone where a more flexible polymer backbone allows the cooperative catalysis of two Cu sites. The second coordination sphere provided by the folded polymer that has been less studied is therefore critical in the design of active mimics of metalloenzymes.

Optimal Affinity Enhancement by a Conserved Flexible Linker Controls p53 Mimicry in MdmX

MdmX contains an intramolecular binding motif that mimics the binding of the p53 tumor suppressor. This intramolecular binding motif is connected to the p53 binding domain of MdmX by a conserved flexible linker that is 85 residues long. The sequence of this flexible linker has an identity of 51% based on multiple protein sequence alignments of 52 MdmX homologs. We used polymer statistics to estimate a global KD value for p53 binding to MdmX in the presence of the flexible linker and the intramolecular binding motif by assuming the flexible linker behaves as a wormlike chain. The global KD estimated from the wormlike chain modeling was nearly identical to the value measured using isothermal titration calorimetry. According to our calculations and measurements, the intramolecular binding motif reduces the apparent affinity of p53 for MdmX by a factor of 400. This study promotes a more quantitative understanding of the role that flexible linkers play in intramolecular binding and provides valuable information to further studies of cellular inhibition of the p53/MdmX interaction.

Checkpoint-Independent Regulation of Origin Firing by Mrc1 through Interaction with Hsk1 Kinase.

Mrc1 is a conserved checkpoint mediator protein that transduces the replication stress signal to the downstream effector kinase. The loss of mrc1 checkpoint activity results in the aberrant activation of late/dormant origins in the presence of hydroxyurea. Mrc1 was also suggested to regulate orders of early origin firing in a checkpoint-independent manner, but its mechanism was unknown. Here we identify HBS (Hsk1 bypass segment) on Mrc1. An ΔHBS mutant does not activate late/dormant origin firing in the presence of hydroxyurea but causes the precocious and enhanced activation of weak early-firing origins during normal S-phase progression and bypasses the requirement for Hsk1 for growth. This may be caused by the disruption of intramolecular binding between HBS and NTHBS (N-terminal target of HBS). Hsk1 binds to Mrc1 through HBS and phosphorylates a segment adjacent to NTHBS, disrupting the intramolecular interaction. We propose that Mrc1 exerts a "brake" on initiation (through intramolecular interactions) and that this brake can be released (upon the loss of intramolecular interactions) by either the Hsk1-mediated phosphorylation of Mrc1 or the deletion of HBS (or a phosphomimic mutation of putative Hsk1 target serine/threonine), which can bypass the function of Hsk1 for growth. The brake mechanism may explain the checkpoint-independent regulation of early origin firing in fission yeast.

Into the linker's DENN: A tyrosine's control of autophagy

The small GTP-binding protein Rab12 plays an important role in the initiation of starvation-induced macroautophagy (autophagy) and is activated by the guanine-nucleotide exchange factor DENND3. However, the molecular mechanism by which DENND3 becomes activated has remained elusive. Xu and McPherson now identify a novel mechanism of DENND3 intramolecular binding that is regulated by the phosphorylation of a single tyrosine residue.

Zlock, a Broadly Applicable Optogenetic Method, Controls Cofilin in Living Cells

The spatial and temporal organization of protein activity controls the flow of information through signaling networks. Optogenetics, the regulation of protein activity with light, has proven very useful to dissect the role of spatio-temporal control by inducing specific protein activities with seconds and microns resolution in living cells. However, current methods are not applicable to many important proteins. Here we describe Zlock, a broadly applicable optogenetic method to control protein or small-peptide activity in living cells using modifications of Zdark (Zdk), a small protein that binds only to the dark state of the LOV2 domain from Phototropin. The LOV2 domain undergoes a reversible conformational change induced by 400-500 nm light. Zdk, derived by screening a library of Z domain variants of protein A, binds selectively to the dark state of LOV2 with dark Kd 10 micromolar. In the “Zlock” system, Zdk and LOV2 are fused to the N- and C- termini of a target protein or small-peptide. In the dark, they bind to one another and cover or distort the active site. Upon irradiation they release one another in less than a second, freeing the active site for target interaction. We have engineered Zdk for the reversible intramolecular binding needed in the Zlock design. We have successfully applied Zlock to generate photoactivatable analogs of important cytoskeletal regulators including cofilin and Alpha Tubulin Acetyltransferase 1 (ATAT). Photoactivation of cofilin and ATAT in live cells controls cell protrusion and microtubule acetylation, and has demonstrated a clear role for cofilin in regulating directionality during cancer cell migration. Current work is focused on ‘caging’ photoactivatable small-peptide inhibitors of Cdc42, PP1, JNK and Gqα, to control endogenous proteins with light.

Correcting mitochondrial fusion by manipulating mitofusin conformations.

Mitochondria are dynamic organelles that exchange contents and undergo remodelling during cyclic fusion and fission. Genetic mutations in MFN2 (the gene encoding mitofusin 2) interrupt mitochondrial fusion and cause the untreatable neurodegenerative condition Charcot-Marie-Tooth disease type 2A (CMT2A). It has not yet been possible to directly modulate mitochondrial fusion, in part because the structural basis of mitofusin function is not completely understood. Here we show that mitofusins adopt either a fusion-constrained or a fusion-permissive molecular conformation, directed by specific intramolecular binding interactions, and demonstrate that mitofusin-dependent mitochondrial fusion can be regulated in mouse cells by targeting these conformational transitions. On the basis of this model, we engineered a cell-permeant minipeptide to destabilize the fusion-constrained conformation of mitofusin and promote the fusion-permissive conformation, reversing mitochondrial abnormalities in cultured fibroblasts and neurons that harbour CMT2A-associated genetic defects. The relationship between the conformational plasticity of mitofusin 2 and mitochondrial dynamism reveals a central mechanism that regulates mitochondrial fusion, the manipulation of which can correct mitochondrial pathology triggered by defective or imbalanced mitochondrial dynamics.

Effects of mutants in bHLH region on structure stability and protein-DNA binding energy in DECs

The human DEC subfamily contains two highly conserved members belonging to basic helix-loop-helix (bHLH) transcription factors. This conserved family is spread widely among various species with the function of regulating various crucial molecular signaling pathways. Due to the significance of DECs for important biological processes, their relationship with diseases and the lack of experimentally proven structures, we have implemented a comparative modeling for the bHLH region of DECs as homodimers with themselves and heterodimers with HES-1. Three mutants with predicted roles in reducing intramolecular binding (H57A, R65A, and LL7879AA in DEC1 and LL7071AA in DEC2) were investigated on DEC monomers. Molecular dynamics (MD) simulations were also employed to evaluate the behavior of the mutant molecules in aqueous solution. The monomer was divided into subregions for accurate investigation. The fluctuation in the basic region of mutants was higher than that of wild-type molecules. The binding energy value between protein and DNA obviously increased in the homodimer harboring R65A mutants, which led to more unstable status between protein and DNA. Thus, the mutant R65A interfered DNA-binding affinity. A study on the spatial structures of wild-type and mutant DECs may facilitate functional prediction for mutation effects and dynamic behavior under various conditions and may ultimately help in targeted drug design.

Direct Demonstration That Loop1 of Scap Binds to Loop7: A CRUCIAL EVENT IN CHOLESTEROL HOMEOSTASIS

Cholesterol homeostasis is mediated by Scap, a polytopic endoplasmic reticulum (ER) protein that transports sterol regulatory element-binding proteins from the ER to Golgi, where they are processed to forms that activate cholesterol synthesis. Scap has eight transmembrane helices and two large luminal loops, designated Loop1 and Loop7. We earlier provided indirect evidence that Loop1 binds to Loop7, allowing Scap to bind COPII proteins for transport in coated vesicles. When ER cholesterol rises, it binds to Loop1. We hypothesized that this causes dissociation from Loop7, abrogating COPII binding. Here we demonstrate direct binding of the two loops when expressed as isolated fragments or as a fusion protein. Expressed alone, Loop1 remained intracellular and membrane-bound. When Loop7 was co-expressed, it bound to Loop1, and the soluble complex was secreted. A Loop1-Loop7 fusion protein was also secreted, and the two loops remained bound when the linker between them was cleaved by a protease. Point mutations that disrupt the Loop1-Loop7 interaction prevented secretion of the Loop1-Loop7 fusion protein. These data provide direct documentation of intramolecular Loop1-Loop7 binding, a central event in cholesterol homeostasis.

Cooperative Control of Caspase Recruitment Domain-containing Protein 11 (CARD11) Signaling by an Unusual Array of Redundant Repressive Elements

Several classes of signaling proteins contain autoinhibitory domains that prevent unwarranted signaling and coordinate the induction of activity in response to external cues. CARD11, a scaffold protein critical for antigen receptor signaling to NF-κB, undergoes autoregulation by a poorly understood inhibitory domain (ID), which keeps CARD11 inactive in the absence of receptor triggering through inhibitory intramolecular interactions. This autoinhibitory strategy makes CARD11 highly susceptible to gain-of-function mutations that are frequently observed in diffuse large B cell lymphoma (DLBCL) and that disrupt ID-mediated autoinhibition, leading to constitutive NF-κB activity, which can promote lymphoma proliferation. Although DLBCL-associated CARD11 mutations in the caspase recruitment domain (CARD), LATCH domain, and coiled coil have been shown to disrupt intramolecular ID binding, surprisingly, no gain-of-function mutations in the ID itself have been reported and validated. In this study, we solve this paradox and report that the CARD11 ID contains an unusual array of four repressive elements that function cooperatively with redundancy to prevent spontaneous NF-κB activation. Our quantitative analysis suggests that potent oncogenic CARD11 mutations must perturb autoinhibition by at least three repressive elements. Our results explain the lack of ID mutations in DLBCL and reveal an unusual autoinhibitory domain structure and strategy for preventing unwarranted scaffold signaling to NF-κB.

Insights into the allosteric regulation of Syk association with receptor ITAM, a multi-state equilibrium.

The phosphorylation of interdomain A (IA), a linker region between tandem SH2 domains of Syk tyrosine kinase, regulates the binding affinity for association of Syk with doubly-phosphorylated ITAM regions of the B cell receptor. The mechanism of this allosteric regulation has been suggested to be a switch from the high-affinity bifunctional binding, mediated through both SH2 domains binding two phosphotyrosine residues of ITAM, to a substantially lower-affinity binding of only one SH2 domain. IA phosphorylation triggers the switch by inducing disorder in IA and weakening the SH2-SH2 interaction. The postulated switch to a single-SH2-domain binding mode is examined using NMR to monitor site-specific binding to each SH2 domain of Syk variants engineered to have IA regions that differ in conformational flexibility. The combined analysis of titration curves and NMR line-shapes provides sufficient information to determine the energetics of inter-molecular binding at each SH2 site along with an intra-molecular binding or isomerization step. A less favorable isomerization equilibrium associated with the changes in the SH2-SH2 conformational ensemble and IA flexibility accounts for the inhibition of Syk association with membrane ITAM regions when IA is phosphorylated, and refutes the proposed switch to single-SH2-domain binding. Syk localizes in the cell through its SH2 interactions, and this basis for allosteric regulation of ITAM association proposes for the first time a phosphorylation-dependent model to regulate Syk binding to alternate receptors and other signaling proteins that differ either in the number of residues separating ITAM phosphotyrosines or by having only one phosphotyrosine, a half ITAM.

Circular Permutation Probes for Illuminating Phosphorylation of Estrogen Receptor.

The present protocol demonstrates a new strategy for imaging ligand-triggered protein phosphorylation using circularly permutated luciferases (cpLuc): (1) a luciferase is first fragmented into two segments for creating new N- and C-terminal ends in the hydrophilic region, (2) the original N- and C-terminal ends are circularly permutated and linked via a GS linker, whereas the new ends made by fragmentation are correspondingly linked with two proteins of interest. When the new ends of the cpLuc are linked with the ligand-binding domain of estrogen receptor (ER LBD) and Src homology two domain of Src (SH2), the estrogen can trigger phosphorylation of the ER LBD and consequent intramolecular ER LBD-SH2 binding. This interaction triggers an approximation of the adjacent fragments of split-cpLuc recovering the enzyme activity. This probe design greatly improves signal-to-noise (S/N) ratios upon tracing weak protein-protein interactions (PPIs) in mammalian cells.

Versatile ruthenium complexes based on 2,2'-bipyridine modified peptoids.

Helical peptoids bearing 2,2'-bipyridine form ruthenium complexes via intermolecular binding to linear peptoid strands or intramolecular binding to a cyclic scaffold. Ru(ii) binding promoted changes in the conformational order of the peptoids, and chiral induction from the peptoids to their metal center was observed.

Hydrogen-Bonded Macrocyclic Supramolecular Systems in Solution and on Surfaces.

Cyclization into closed assemblies is the most recurrent approach to realize the noncovalent synthesis of discrete, well‐defined nanostructures. This review article particularly focuses on the noncovalent synthesis of monocyclic hydrogen‐bonded systems that are self‐assembled from a single molecule with two binding‐sites. Taking advantage of intramolecular binding events, which are favored with respect to intermolecular binding in solution, can afford quantitative amounts of a given supramolecular species under thermodynamic control. The size of the assembly depends on geometric issues such as the monomer structure and the directionality of the binding interaction, whereas the fidelity achieved relies largely on structural preorganization, low degrees of conformational flexibility, and templating effects. Here, we discuss several examples described in the literature in which cycles of different sizes, from dimers to hexamers, are studied by diverse solution or surface characterization techniques.

Water-soluble chiral metallopeptoids.

Metal ions play a significant role in the activity of biological systems including catalysis, recognition and folding. Therefore, introducing metal ions into peptidomimetic oligomers is a potential way for creating biomimetic metal complexes toward applications in sensing, recognition, drug design and catalysis. Herein we report the design, synthesis and characterization of water-soluble chiral N-substituted glycine oligomers, "peptoids," with one and two distinct intramolecular binding sites for metal ions such as copper and cobalt. We demonstrate for the first time the incorporation of the chiral hydrophilic group (S)-(+)-1-methoxy-2-propylamine (Nsmp) within peptoid sequences, which provides both chirality and water solubility. Two peptoids, a heptamer, and a dodecamer bearing two and four 8-hydroxyquinoline (HQ) groups respectively as metal-binding ligands, were synthesized on solid support using the submonomer approach. Using UV-titrations and ESI-MS analysis we demonstrate the creation of a novel metallopeptoid bearing two metal ions in distinct binding sites via intramolecular chelation. Exciton couplet circular dichroism (ECCD) demonstrated chiral induction from the chiral non-helical peptoids to the metal centers.

Activating Mutations Affecting the Dbl Homology Domain of SOS2 Cause Noonan Syndrome.

The RASopathies constitute a family of autosomal-dominant disorders whose major features include facial dysmorphism, cardiac defects, reduced postnatal growth, variable cognitive deficits, ectodermal and skeletal anomalies, and susceptibility to certain malignancies. Noonan syndrome (NS), the commonest RASopathy, is genetically heterogeneous and caused by functional dysregulation of signal transducers and regulatory proteins with roles in the RAS/extracellular signal-regulated kinase (ERK) signal transduction pathway. Mutations in known disease genes account for approximately 80% of affected individuals. Here, we report that missense mutations altering Son of Sevenless, Drosophila, homolog 2 (SOS2), which encodes a RAS guanine nucleotide exchange factor, occur in a small percentage of subjects with NS. Four missense mutations were identified in five unrelated sporadic cases and families transmitting NS. Disease-causing mutations affected three conserved residues located in the Dbl homology (DH) domain, of which two are directly involved in the intramolecular binding network maintaining SOS2 in its autoinhibited conformation. All mutations were found to promote enhanced signaling from RAS to ERK. Similar to NS-causing SOS1 mutations, the phenotype associated with SOS2 defects is characterized by normal development and growth, as well as marked ectodermal involvement. Unlike SOS1 mutations, however, those in SOS2 are restricted to the DH domain.

Intramolecular Binding of the Rad9 C Terminus in the Checkpoint Clamp Rad9-Hus1-Rad1 Is Closely Linked with Its DNA Binding

The human checkpoint clamp Rad9-Hus1-Rad1 (9-1-1) is loaded onto chromatin by its loader complex, Rad17-RFC, following DNA damage. The 120-amino acid (aa) stretch of the Rad9 C terminus (C-tail) is unstructured and projects from the core ring structure (CRS). Recent studies showed that 9-1-1 and CRS bind DNA independently of Rad17-RFC. The DNA-binding affinity of mutant 9(ΔC)-1-1, which lacked the Rad9 C-tail, was much higher than that of wild-type 9-1-1, suggesting that 9-1-1 has intrinsic DNA binding activity that manifests in the absence of the C-tail. C-tail added in trans interacted with CRS and prevented it from binding to DNA. We narrowed down the amino acid sequence in the C-tail necessary for CRS binding to a 15-aa stretch harboring two conserved consecutive phenylalanine residues. We prepared 9-1-1 mutants containing the variant C-tail deficient for CRS binding, and we demonstrated that the mutant form restored DNA binding as efficiently as 9(ΔC)-1-1. Furthermore, we mapped the sequence necessary for TopBP1 binding within the same 15-aa stretch, demonstrating that TopBP1 and CRS share the same binding region in the C-tail. Indeed, we observed their competitive binding to the C-tail with purified proteins. The importance of interaction between 9-1-1 and TopBP1 for DNA damage signaling suggests that the competitive interactions of TopBP1 and CRS with the C-tail will be crucial for the activation mechanism.

Molecular dynamics study of the effects of calcium ions on the conformational properties of comb-like poly(acrylic acid-co-methyl allyl polyoxyethylene ether)

All-atom molecular dynamics simulations were employed to study the microscopic conformational properties of three kinds of comb-like poly(acrylic acid-co-methyl allyl polyoxyethylene ether) (P(AA-co-MAPEG)) in solution. Two different systems, which contained single chain and two chains respectively, were studied, and the binding types of calcium ions (Ca2+) to carboxylate groups (–COO−) were analyzed. For the systems containing a single chain, as the concentration of Ca2+ increased, the value of the radius of gyration, Rg, for P(AA-co-MAPEG) (4:1) (4:1 represented the monomer ratios of acrylic acid to polyoxyethylene methyl allyl ether, the same description below) chain sharply decreased in Ca2+ solution because Ca2+ weakened the repulsive electrostatic interactions between the charged –COO− while hardly interacted with –COO− directly (e.g. coordination). And the values of Rg for the P(AA-co-MAPEG) (6:1) chain and P(AA-co-MAPEG) (9:1) chain changed slightly because Ca2+ easily interacted with the –COO−, and the polymer chains exhibited a more rigid conformation. For the systems containing two chains, due to two competing factors, the solvation of –COO− and steric hindrance induced by side chains, it was favorable for P(AA-co-MAPEG) (6:1) chains to approach each other to form intermolecular Ca2+ bridges. For comb-like polyelectrolyte, intermolecular binding was difficult to form than intramolecular binding. And among all the possible intramolecular binding modes, the type of Ca2+ binding to two oxygen atoms of adjacent –COO− was the most favorable.