Well-defined Conformation Research Articles

ChemInform Abstract: Organic Foldamers and Helices

AbstractReview: 66 refs.

Multidomain Protein Solves the Folding Problem by Multifunnel Combined Landscape: Theoretical Investigation of a Y-Family DNA Polymerase

Approximately three-fourths of eukaryotic proteins are composed of multiple independently folded domains. However, much of our understanding is based on single domain proteins or isolated domains whose studies directly lead to well-known energy landscape theory in which proteins fold by navigating through a funneled energy landscape toward native structure ensembles. The degrees of freedom for proteins with multiple domains are many orders of magnitude larger than that for single domain proteins. Now, the question arises: How do the multidomain proteins solve the "protein folding problem"? Here, we specifically address this issue by exploring the structure folding relationship of Sulfolobus solfataricus DNA polymerase IV (DPO4), a prototype Y-family DNA polymerase which contains a polymerase core consisting of a palm (P domain), a finger (F domain), and a thumb domain (T domain) in addition to a little finger domain (LF domain). The theoretical results are in good agreement with the experimental data and lead to several theoretical predictions. Finally, we propose that for rapid folding into well-defined conformations which carry out the biological functions, four-domain DPO4 employs a divide-and-conquer strategy, that is, combining multiple individual folding funnels into a single funnel (domains fold independently and then coalesce). In this way, the degrees of freedom for multidomain proteins are polynomial rather than exponential, and the conformational search process can be reduced effectively from a large to a smaller time scale.

β-Barrel Mobility Underlies Closure of the Voltage-Dependent Anion Channel

The voltage-dependent anion channel (VDAC) is themajor protein in the outer mitochondrial membrane, where it mediates transport of ATP and ADP. Changes in its permeability, induced by voltage or apoptosis-related proteins, have been implicated in apoptotic pathways. The three-dimensional structure of VDAC has recently been determined asa 19-stranded β-barrel with an in-lying N-terminal helix. However, its gating mechanism is still unclear. Using solid-state NMR spectroscopy, molecular dynamics simulations, and electrophysiology, we show that deletion of the rigid N-terminal helix sharply increases overall motion in VDAC's β-barrel, resulting in elliptic, semicollapsed barrel shapes. These states quantitatively reproduce conductance and selectivity of the closed VDAC conformation. Mutation of the N-terminal helix leads to a phenotype intermediate to the open and closed states. These data suggest that the N-terminal helix controls entry into elliptic β-barrel states which underlie VDAC closure. Our results also indicate that β-barrel channels are intrinsically flexible.

Structural basis for substrate specificity and catalysis of human histone acetyltransferase 1

Histone acetyltransferase 1 is the founding member of the histone acetyltransferase superfamily and catalyzes lysine acetylation of newly synthesized histone H4. Here we report a 1.9-Å resolution crystal structure of human histone acetyltransferase 1 in complex with acetyl coenzyme A and histone H4 peptide. The crystal structure reveals that the cofactor and the side chain of lysine 12 of histone H4 peptide are placed in the canyon between the central and C-terminal domains. Histone H4 peptide adopts a well-defined conformation and establishes an extensive set of interactions with the enzyme including invariant residues Glu64 and Trp199, which together govern substrate-binding specificity of histone acetyltransferase 1. Our structure-guided enzyme kinetic study further demonstrates a cumulative effect of the active-site residues Glu187, Glu276, and Asp277 on deprotonation of the ε-amino group of reactive Lys12 for direct attack of the acetyl group of the cofactor.

Putting a Stop to l,d-Transpeptidases

In this issue of Structure, Lecoq et al. investigated the structural and dynamic basis for the unexpected inhibition of peptidoglycan-crosslinking l,d-transpeptidases by carbapenem antibiotics. In addition to defining a neutral thiol-imidazole catalytic triad, their studies revealed extensive induced motions upon formation of a long-live covalent drug-enzyme complex.

Cyclic RGD Peptidomimetics Containing Bifunctional Diketopiperazine Scaffolds as New Potent Integrin Ligands

The synthesis of eight bifunctional diketopiperazine (DKP) scaffolds is described; these were formally derived from 2,3-diaminopropionic acid and aspartic acid (DKP-1-DKP-7) or glutamic acid (DKP-8) and feature an amine and a carboxylic acid functional group. The scaffolds differ in the configuration at the two stereocenters and the substitution at the diketopiperazinic nitrogen atoms. The bifunctional diketopiperazines were introduced into eight cyclic peptidomimetics containing the Arg-Gly-Asp (RGD) sequence. The resulting RGD peptidomimetics were screened for their ability to inhibit biotinylated vitronectin binding to the purified integrins α(v)β(3) and α(v)β(5), which are involved in tumor angiogenesis. Nanomolar IC(50) values were obtained for the RGD peptidomimetics derived from trans DKP scaffolds (DKP-2-DKP-8). Conformational studies of the cyclic RGD peptidomimetics by (1)H NMR spectroscopy experiments (VT-NMR and NOESY spectroscopy) in aqueous solution and Monte Carlo/Stochastic Dynamics (MC/SD) simulations revealed that the highest affinity ligands display well-defined preferred conformations featuring intramolecular hydrogen-bonded turn motifs and an extended arrangement of the RGD sequence [Cβ(Arg)-Cβ(Asp) average distance ≥8.8 Å]. Docking studies were performed, starting from the representative conformations obtained from the MC/SD simulations and taking as a reference model the crystal structure of the extracellular segment of integrin α(v)β(3) complexed with the cyclic pentapeptide, Cilengitide. The highest affinity ligands produced top-ranked poses conserving all the important interactions of the X-ray complex.

The Mechanisms of RNA SHAPE Chemistry

The biological functions of RNA are ultimately governed by the local environment at each nucleotide. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry is a powerful approach for measuring nucleotide structure and dynamics in diverse biological environments. SHAPE reagents acylate the 2'-hydroxyl group at flexible nucleotides because unconstrained nucleotides preferentially sample rare conformations that enhance the nucleophilicity of the 2'-hydroxyl. The critical corollary is that some constrained nucleotides must be poised for efficient reaction at the 2'-hydroxyl group. To identify such nucleotides, we performed SHAPE on intact crystals of the Escherichia coli ribosome, monitored the reactivity of 1490 nucleotides in 16S rRNA, and examined those nucleotides that were hyper-reactive toward SHAPE and had well-defined crystallographic conformations. Analysis of these conformations revealed that 2'-hydroxyl reactivity is broadly facilitated by general base catalysis involving multiple RNA functional groups and by two specific orientations of the bridging 3'-phosphate group. Nucleotide analog studies confirmed the contributions of these mechanisms to SHAPE reactivity. These results provide a strong mechanistic explanation for the relationship between SHAPE reactivity and local RNA dynamics and will facilitate interpretation of SHAPE information in the many technologies that make use of this chemistry.

Structure–activity studies of lGnRH‐III through rational amino acid substitution and NMR conformational studies

Lamprey gonadotropin-releasing hormone type III (lGnRH-III) is an isoform of GnRH isolated from the sea lamprey (Petromyzon marinus) with negligible endocrine activity in mammalian systems. Data concerning the superior direct anticancer activity of lGnRH-III have been published, raising questions on the structure-activity relationship. We synthesized 21 lGnRH-III analogs with rational amino acid substitutions and studied their effect on PC3 and LNCaP prostate cancer cell proliferation. Our results question the importance of the acidic charge of Asp⁶ for the antiproliferative activity and indicate the significance of the stereochemistry of Trp in positions 3 and 7. Furthermore, conjugation of an acetyl-group to the side chain of Lys⁸ or side chain cyclization of amino acids 1-8 increased the antiproliferative activity of lGnRH-III demonstrating that the proposed salt bridge between Asp⁶ and Lys⁸ is not crucial. Conformational studies of lGnRH-III were performed through NMR spectroscopy, and the solution structure of GnRH-I was solved. In solution, lGnRH-III adopts an extended backbone conformation in contrast to the well-defined β-turn conformation of GnRH-I.

Conformational modulation of Ant–Pro oligomers using chirality alteration of proline residues

Structural modulation of Ant-Pro (anthranilic acid-proline) oligomers has been carried out by chirality alteration of the proline residues. The results suggest that the chirality altered oligomers show well-defined helical conformation featuring nine-membered hydrogen bonding interactions - without compromising conformational rigidity.

Cn‐AMP1: A new promiscuous peptide with potential for microbial infections treatment

The antimicrobial peptides (AMPs) are evolutionarily ancient molecules that act as components of the innate immune system. Recently, it was demonstrated that a single AMP can perform various functions; this ability is known as "peptide promiscuity." However, little is known about promiscuity in plant AMPs without disulfide bonds. This study was carried out to evaluate the promiscuity of Cn-AMP1: a promising disulfide-free plant peptide with reduced size and cationic and hydrophobic properties. Its activity against human pathogenic bacteria and fungal pathogens, as well as its in vitro immunostimulatory activity and effects on cancerous and healthy mammalian cell proliferation were studied here. Cn-AMP1 exerts antimicrobial effects against Gram-positive bacteria, Gram-negative bacteria, and fungi. Moreover, tumor cell viability activity in Caco-2 cells, as well as immunostimulatory activity by evaluating upregulated inflammatory-cytokine secretion by monocytes was also positively observed. Cn-AMP1 does not exhibit a well-defined conformation in aqueous solution and probably undergoes a 3(10)-helix transition in hydrophobic environments. The experimental results support the promiscuous activity of Cn-AMP1, presenting a wide range of activities, including antibacterial, antifungal, and immunostimulatory activity. In the future, Cn-AMP1 should be used in the development of novel biopharmaceuticals, mainly due to its reduced size and broad spectrum of activity.

Conformational Change in the ATPase-Gate of Topoisomerase VI Induced by Nucleotide and DNA

Archaeal topoisomerase VI catalyzes the relaxation and decatenation of DNA. In an ATP-dependent manner it transports a DNA double strand through a gap in a second duplex by a sequential opening and closing of two gates. Conformational change in the ATPase-gate of M. mazei topoisomerase VI was monitored in single molecule FRET experiments, using fluorescently labeled enzyme with one dye attached to each nucleotide-binding domain.We have observed four different conformational states of the ATP-binding domains: In the absence of nucleotide or DNA the ATPase-gate exhibits conformational flexibility, indicating gate opening and closing. Binding of supercoiled plasmid to TopoVI forces the ATPase-gate to open up even wider, although considerable flexibility of the domains is retained; both these states have been proposed on the basis of two crystal structures of intact TopoVI holoenzymes, showing a closed and an open gate conformation. Addition of ADPNP - a non-hydrolysable ATP analog - induces a well-defined conformation of the ATPase domains close to each other, indicating dimerization; this is in agreement with crystal structure from isolated TopoVI-B domains which show tight association when bound to ADPNP. Addition of both nucleotide and plasmid immobilizes the domains in a conformation different from the one observed for the closed gate, indicating that the presence of a DNA segment in the central cavity induces physical strain to the TopoVI complex; this state has not been proposed so far, but should be due to an internal rotation in the ATP-binding domains mediated by a conserved lysine residue acting as a gamma-phosphate sensor.Topoisomerase VI exhibits a different conformational behavior than type II topoisomerases (e.g. gyrase) in that it does not show DNA-induced pre-closure but rather opening of the gate in presence of a supercoiled DNA.

Molecular architecture of heparin and heparan sulfate: Recent developments in solution structural studies

The study of the relationship between the complex structures and numerous physiological functions of the glycosaminoglycans (GAGs) heparin and heparan sulfate (HS) has continued to thrive in the past decade. Though it is clear that the monosaccharide sequences of these polysaccharides must determine their ability to modulate the action of growth factors, morphogens, chemokines, cytokines, and many other extracellular proteins, the exact details of this dependence still prove elusive. Sequence determines the 3D structure of GAGs at more than one level; detailed sequences of highly sulfated regions may influence affinity for specific proteins in some cases, but in addition attention has been called to the importance of the length and spacing of these highly sulfated sequences, which are separated by unsulfated domains. Within the sulfated “S-domains”, the internal dynamics of the conformationally flexible iduronate pyranose ring have continued to interest NMR spectroscopists and molecular modelers. New studies of the relative degrees of flexibility of sulfated and unsulfated domains lead to an overall model of heparin/HS in which protein-binding, highly sulfated S-domains with well-defined conformations are separated by more flexible NA-domains.

Structural insights into the substrate specificity of bacterial copper amine oxidase obtained by using irreversible inhibitors

Copper amine oxidases (CAOs) catalyse the oxidation of various aliphatic amines to the corresponding aldehydes, ammonia and hydrogen peroxide. Although CAOs from various organisms share a highly conserved active-site structure including a protein-derived cofactor, topa quinone (TPQ), their substrate specificities differ considerably. To obtain structural insights into the substrate specificity of a CAO from Arthrobacter globiformis (AGAO), we have determined the X-ray crystal structures of AGAO complexed with irreversible inhibitors that form covalent adducts with TPQ. Three hydrazine derivatives, benzylhydrazine (BHZ), 4-hydroxybenzylhydrazine (4-OH-BHZ) and phenylhydrazine (PHZ) formed predominantly a hydrazone adduct, which is structurally analogous to the substrate Schiff base of TPQ formed during the catalytic reaction. With BHZ and 4-OH-BHZ, but not with PHZ, the inhibitor aromatic ring is bound to a hydrophobic cavity near the active site in a well-defined conformation. Furthermore, the hydrogen atom on the hydrazone nitrogen is located closer to the catalytic base in the BHZ and 4-OH-BHZ adducts than in the PHZ adduct. These results correlate well with the reactivity of 2-phenylethylamine and tyramine as preferred substrates for AGAO and also explain why benzylamine is a poor substrate with markedly decreased rate constants for the steps of proton abstraction and the following hydrolysis.

Regulation of integrin affinity on cell surfaces

Lymphocyte activation triggers adhesiveness of lymphocyte function-associated antigen-1 (LFA-1; integrin α(L)β(2)) for intercellular adhesion molecules (ICAMs) on endothelia or antigen-presenting cells. Whether the activation signal, after transmission through multiple domains to the ligand-binding αI domain, results in affinity changes for ligand has been hotly debated. Here, we present the first comprehensive measurements of LFA-1 affinities on T lymphocytes for ICAM-1 under a broad array of activating conditions. Only a modest increase in affinity for soluble ligand was detected after activation by chemokine or T-cell receptor ligation, conditions that primed LFA-1 and robustly induced lymphocyte adhesion to ICAM-1 substrates. By stabilizing well-defined LFA-1 conformations by Fab, we demonstrate the absolute requirement of the open LFA-1 headpiece for adhesiveness and high affinity. Interaction of primed LFA-1 with immobilized but not soluble ICAM-1 triggers energy-dependent affinity maturation of LFA-1 to an adhesive, high affinity state. Our results lend support to the traction or translational motion dependence of integrin activation.

Nitrogen and Oxygen Bridged Calixaromatics: Synthesis, Structure, Functionalization, and Molecular Recognition

Pedersen, Lehn, and Cram established supramolecular chemistry through their pioneering work with crown ethers, cryptands, and spherands. Since then, the hallmark of supramolecular science has been an increasing sophistication in the design and construction of macrocyclic molecules, as manifested in cyclodextrin derivatives, calixarenes, resorcinarenes, cyclotriveratrylenes, cucurbiturils, calixpyrroles, cyclophanes, and many other examples. Indeed, macrocyclic compounds provide unique models for the study of noncovalent molecular interactions. They also constitute building blocks for constructing high-level molecular and supramolecular architectures and fabricating molecular devices and advanced materials. As a postgraduate in the Huang laboratory in the late 1980s, I became interested in the calix[n]arenes because of their unique conformational structures and versatile complexation properties. The notion of introducing heteroatoms, and particularly nitrogen, into the bridging position of conventional calixarenes was particularly intriguing. Nitrogen, unlike methylene, can adopt either an sp(2) or sp(3) electronic configuration, providing different conjugation systems with adjacent aromatic rings. Consequently, depending on the configuration and conjugation, a range of C-N bond lengths and C-N-C bond angles is possible. The conformation and cavity size in heteroatom-bridged calixarenes might thus be tuned through the bridging heteroatoms and the number of aromatic rings. Furthermore, because heteroatom linkages significantly affect the electron density and distribution on aromatic rings, the electronic features of macrocyclic cavities might be regulated by heteroatoms. Given the essentially limitless combinations possible, only synthetic hurdles would prevent access to numerous diverse heteracalixaromatics. We began a systematic study on nitrogen- and oxygen-bridged calixarenes in 2000, years later than originally envisioned. Before this study, very few heteracalixaromatics had been reported, owing to the formidable synthetic challenges involved. Apart from thiacalixarene, the synthesis of nitrogen- and oxygen-bridged calixarenes appeared very difficult. But since our first publications in 2004, we have been delighted to see the rapid and tremendous development of the supramolecular chemistry of this new generation of macrocycles. In this Account, I summarize the synthesis of N- and O-bridged calixaromatics and their regiospecific functionalization on the rims and bridging positions, focusing on the fragment coupling approach and contributions from our laboratory. I describe the construction of molecular cages based on heteracalixaromatics and discuss the effect of both bridging heteroatoms and substituents on macrocyclic conformations and cavity sizes. Molecular recognition of neutral organic molecules and charged guest species is also demonstrated. The easy accessibility, rich molecular diversity, unique conformation, and cavity tunability of heteracalixaromatics make them invaluable macrocycles for research in supramolecular chemistry. New heteracalixaromatics, with well-defined conformations and cavity properties, will provide powerful tools for probing noncovalent interactions, leading to the development of new molecular sensing and imaging systems. Multicomponent molecular self-assembly of heteracalixaromatics as functional modules with metals, metal clusters, or charge-neutral species should result in multidimensional solid and soft materials with diverse applications. The profitable incorporation of heteracalixaromatics into molecular devices can also be anticipated in the future. Moreover, the construction of enantiopure, inherently chiral heteracalixaromatics should provide important applications in chiral recognition and asymmetric catalysis.

Do Commercially Available Metal Salts Mediate Calixarene Formation via Hydrogen-Bonded Dimers?

In this article we report the first example of a Lewis acid promoted, one-pot, Brønsted acid free, high-yielding synthesis of the calixarene macrocycle from the "monomer" p-tert-butylphenol. We report that when a commercially available metal salt (Lewis acid) is incorporated within the calixarene-forming reaction, a certain amount of control over the size of the calixarenes produced can be gained. Although a detailed mechanistic rationale on how the macrocycle is assembled is unclear, what is evident from this work is that the metal cation, the counteranion, and the oxidation state of the salt employed are all important contributors to the outcome of the reaction process. Indeed, evidence to date suggests that a subtle "symbiotic" relationship exists between the metal cation, its oxidation state, and the anion that allows the efficient transformation of the "monomeric" p-tert-butylphenol into linear oligomers and, ultimately, into macrocyclic calixarenes. Athough the metal salt mediated process described herein is efficient and high-yielding, what is also fundamentally important is that a comprehensive mechanistic understanding of how the calixarenes are assembled be accrued. Searching for possible indicators or clues, we propose that oligomeric methylene-linked phenolic entities are initially formed and that these, we tentatively suggest, generate metal and/or anion hydrogen-bonded supramolecular intermediates. It is possible that the preorganization of the linear polyphenolic oligomers allows the formation of hydrogen-bonded structures which, critically, result in the formation of supramolecular assemblies that are subsequently "stitched" together, generating the p-tert-butylcalix[n]arenes (n = 4-9) in excellent yields. Substantiating the possibility that hydrogen-bonded entities are generated (and that these subsequently afford metal-templated assemblies), we make reference to a seldom cited 1962 Nature publication that reported the propensity of polyphenolic linear oligomers to form "well-defined intramolecularly hydrogen-bonded conformations".

A Nonpeptidic Reverse-Turn Scaffold Stabilized by Urea-Based Dual Intramolecular Hydrogen Bonding

A novel nonpeptidic reverse-turn scaffold containing urea fragments that are connected by a conformationally constrained D-prolyl-cis-1,2-diaminocyclohexane (D-Pro-DACH) linker is reported. The scaffold adopts a well-defined reverse-turn conformation that is stabilized by dual intramolecular hydrogen bonding in both solution and solid states.

The expanding view of protein–protein interactions: complexes involving intrinsically disordered proteins

A frequently neglected aspect of protein–protein interactions is flexibility. Small-scale fluctuations are present even in globular proteins, and alternative conformations can have a significant influence on the binding process. However, flexibility becomes highly prominent in complexes involving intrinsically disordered proteins. The importance of disordered regions in protein interactions has been recognized only relatively recently. In this survey we examine the basic properties of the complexes of disordered and ordered proteins from three different directions. The comparison of the interface properties shows that although disordered proteins can also adopt well-defined conformations in their bound form, their inherently dynamic nature is cast into their complexes. Furthermore, an overview of prediction methods indicates that disordered proteins as well as their binding regions can be recognized from the amino acid sequence by capturing the basic biophysical properties of these segments. Finally, we propose the generalization of the ‘energy landscape model’ for the description of complex formation that can help to put the various types of protein associations on a common ground.

Cyclic Tritrpticin Analogs with Distinct Biological Activities.

Tritrpticin is a Trp-, Arg-, and Pro-rich cathelicidin peptide with promising antimicrobial activity. Cyclic analogs of tritrpticin were designed using two different approaches: circularization of the backbone by a head-to-tail peptide bond (TritrpCyc) or disulfide bridging between two Cys residues introduced at the termini of the peptide (TritrpDisu). Compared to the parent peptide, TritrpCyc has greatly improved therapeutic potential, showing stronger bactericidal activities and diminished hemolytic activity. Unexpectedly, the opposite effect was observed for TritrpDisu, which has lost its antimicrobial activity and is very hemolytic. In a membrane mimetic environment, NMR spectra show that TritrpDisu adopts an amphipathic turn-turn structure similar to linear tritrpticin. The structure of membrane-bound TritrpCyc has some similarity to that of TritrpDisu; however, the lipid interactions were not sufficient to restrain the structure of the former peptide in a single well-defined conformation. To help explain the distinct biological properties of the analogs, experiments investigating alternative antimicrobial targets were pursued: the membrane bilayer, lipopolysaccharides, and DNA. Although the hemolytic activity of TritrpDisu can be explained by the peptide's ability to induce higher leakage from the model mammalian membranes, TritrpCyc and TritrpDisu show no significant differences in these functional assays. Overall, our studies show that TritrpCyc holds great promise as a candidate for further development toward antimicrobial therapy.

Induced Conformational Changes in the Activation of the Pseudomonas aeruginosa type III Toxin, ExoU

ExoU is a 74-kDa, water-soluble toxin injected directly into mammalian cells through the type III secretion system of the opportunistic pathogen, Pseudomonas aeruginosa. Previous studies have shown that ExoU is a Ca 2+-independent phospholipase that requires a eukaryotic protein cofactor. One protein capable of activating ExoU and serving as a required cofactor was identified by biochemical and proteomic methods as superoxide dismutase (SOD1). In these studies, we carried out site-directed spin-labeling electron paramagnetic resonance spectroscopy to examine the effects of SOD1 and substrate liposomes on the structure and dynamics of ExoU. Local conformational changes within the catalytic site were observed in the presence of substrate liposomes, and were enhanced by the addition of SOD1 in a concentration-dependent manner. Conformational changes in the C-terminal domain of ExoU were observed upon addition of cofactor, even in the absence of liposomes. Double electron-electron resonance experiments indicated that ExoU samples multiple conformations in the resting state. In contrast, addition of SOD1 induced ExoU to adopt a single, well-defined conformation. These studies provide, to our knowledge, the first direct evidence for cofactor- and membrane-induced conformational changes in the mechanism of activation of ExoU.