Intermolecular Linkages Research Articles

The Mechanism of Fibril Formation of a Non-inhibitory Serpin Ovalbumin Revealed by the Identification of Amyloidogenic Core Regions

Ovalbumin (OVA), a non-inhibitory member of the serpin superfamily, forms fibrillar aggregates upon heat-induced denaturation. Recent studies suggested that OVA fibrils are generated by a mechanism similar to that of amyloid fibril formation, which is distinct from polymerization mechanisms proposed for other serpins. In this study, we provide new insights into the mechanism of OVA fibril formation through identification of amyloidogenic core regions using synthetic peptide fragments, site-directed mutagenesis, and limited proteolysis. OVA possesses a single disulfide bond between Cys(73) and Cys(120) in the N-terminal helical region of the protein. Heat treatment of disulfide-reduced OVA resulted in the formation of long straight fibrils that are distinct from the semiflexible fibrils formed from OVA with an intact disulfide. Computer predictions suggest that helix B (hB) of the N-terminal region, strand 3A, and strands 4-5B are highly β-aggregation-prone regions. These predictions were confirmed by the fact that synthetic peptides corresponding to these regions formed amyloid fibrils. Site-directed mutagenesis of OVA indicated that V41A substitution in hB interfered with the formation of fibrils. Co-incubation of a soluble peptide fragment of hB with the disulfide-intact full-length OVA consistently promoted formation of long straight fibrils. In addition, the N-terminal helical region of the heat-induced fibril of OVA was protected from limited proteolysis. These results indicate that the heat-induced fibril formation of OVA occurs by a mechanism involving transformation of the N-terminal helical region of the protein to β-strands, thereby forming sequential intermolecular linkages.

ChemInform Abstract: Supramolecular Surface‐Confined Architectures Created by Self‐Assembly of Triangular Phenylene—Ethynylene Macrocycles via van der Waals Interaction.

AbstractReview: 77 refs.

Conformational polymorphism of the molecular complex of 3-fluorobenzoic acid with 4-acetylpyridine

Two polymorphs of the molecular complex formed between 3-fluorobenzoic acid with 4-acetylpyridine are described and found to be based upon the same dimeric supramolecular construct. The conformational freedom around the hydrogen bond results in a 180° rotation about this intermolecular link, distinguishing the polymorphs and affecting the packing of the dimeric units. The two polymorphs are fully characterised by single crystal X-ray and neutron diffraction and quantum mechanical calculations. There is evidence of structured crystal growth defects in both polymorphic crystals via observation of diffuse scattering and a disorder model for the average structure of Form I, which can be interpreted as a mixing of the two dimer conformations. The similarity of energy of the distinct dimeric units, supporting their likely co-existence, has been verified by periodic quantum chemical calculations.

The yeast cell fusion protein Prm1p requires covalent dimerization to promote membrane fusion.

Prm1p is a multipass membrane protein that promotes plasma membrane fusion during yeast mating. The mechanism by which Prm1p and other putative regulators of developmentally controlled cell-cell fusion events facilitate membrane fusion has remained largely elusive. Here, we report that Prm1p forms covalently linked homodimers. Covalent Prm1p dimer formation occurs via intermolecular disulfide bonds of two cysteines, Cys-120 and Cys-545. PRM1 mutants in which these cysteines have been substituted are fusion defective. These PRM1 mutants are normally expressed, retain homotypic interaction and can traffic to the fusion zone. Because prm1-C120S and prm1-C545S mutants can form covalent dimers when coexpressed with wild-type PRM1, an intermolecular C120-C545 disulfide linkage is inferred. Cys-120 is adjacent to a highly conserved hydrophobic domain. Mutation of a charged residue within this hydrophobic domain abrogates formation of covalent dimers, trafficking to the fusion zone, and fusion-promoting activity. The importance of intermolecular disulfide bonding informs models regarding the mechanism of Prm1-mediated cell-cell fusion.

Novel conopeptides in a form of disulfide-crosslinked dimer

In our present work, seven conotoxins and conopeptides were cloned from four cone snail species based on the M-superfamily signal peptides. Among them, two conopeptides, Vt3.1 and Vt3.2, showed unusual sequence characteristics. Both of them contained two cysteines that are separated by just one non-cysteine residue. In vitro, the chemically synthesized Vt3.1 formed dimers with different intermolecular disulfide linkages. Only the dimer with crossed disulfides showed bioactivity when injected into the intraventricular region of mice brains. Therefore, Vt3.1 and Vt3.2 represent a new group of conopeptides that form disulfide-crosslinked dimers in vitro and probably in vivo.

Model reactions for insect cuticle sclerotization: Participation of amino groups in the cross-linking of Manduca sexta cuticle protein MsCP36

Current theories of sclerotization center on protein cross-linking and dehydration as major factors in the hardening and stability of the insect cuticle. Several studies have reported the identification of catechol-amino acid adducts from sclerotizing cuticle involving histidine, lysine, and tyrosine, though there have been no reports of a catechol linked between two amino acid residues. Previously, we reported an in vitro model system for sclerotization and observed that stable protein oligomers were formed, presumably through cross-links with oxidized catecholamines [Insect Biochem. Mol. Biol. (2006) 36, 353–365]. Using site-directed mutagenesis we created a mutant lacking histidine, rMsCP36(H65A/H178A), to investigate the possible involvement of the two histidine residues of MsCP36 in cross-linking. Surprisingly, this alteration had little or no effect on the formation of protein oligomers as determined by SDS-PAGE analysis. Blocking of the free amino groups in lysyl side chains and the amino-terminus by succinylation diminished, but did not eliminate, cross-linking of either rMsCP36 or rMsCP36(H65A/H178A). We also examined the possibility that cross-linking was due to intermolecular dityrosine linkages. Immunoblot analysis utilizing a monoclonal antibody known to recognize peptidyl dityrosine indicated that dityrosyl cross-links were present. Taken together, these results indicate that lysyl residues are important for the cross-linking of the cuticle protein rMsCP36, but that additional residues other than histidine can also contribute.

Correlations between structure and magnetism of three N,N′-ethylene-bis(3-methoxysalicylideneimine) gadolinium complexes

Three Salen-like gadolinium complexes, namely, mononuclear (4f) complex [{H 2 L}Gd(NO 3 ) 3 ] ( 1 ), heterodinuclear (3d–4f) complex [{LCu}Gd(NO 3 ) 3 ]·0.25H 2 O ( 2 ) and dimeric heterotrinuclear (3d–4f–3d′) complex [{LCu}Gd(H 2 O) 3 {Fe(CN) 6 }] 2 ·6H 2 O ( 3 ) [H 2 L = N , N ′-ethylene-bis(3-methoxysalicylideneimine)] have been synthesized by stepwise reactions. X-ray diffraction analysis reveals that 1 is of a discrete structure in which H 2 L coordinates to gadolinium ion through O 2 O 2 moiety. Then, addition of Cu(Ac) 2 ·H 2 O to the mononuclear lanthanide complex yields expected heterodinuclear (3d–4f) complexes [{LCu}Gd(NO 3 ) 3 ]. 3 features a unique 1D ladder-like topology structure through the intermolecular double links of Cu–N bonds. The measurement of variable-temperature magnetic susceptibility reveals that complex 1 exhibits antiferromagnetic interaction while 2 and 3 exhibit ferromagnetic interaction between spin carriers. The correlations between the structure and magnetism are described and discussed.

Physically Networked Polymers: Materials that change with their environment

Polymer networks have continuity of molecular and intermolecular links throughout their structure. These links can be established by covalent, polar or dispersive forces. The choice of link depends on whether a permanent or a reversible structure is required. The continuous network and matrix phase may be different, either chemically or physically, if there is identifiably separate phases. When network formation is through a filler a percolation threshold concentration must be exceeded. Agglomeration of the filler will produce a non-linear strain response. When the matrix phase is of distinct chemistry and physically it can be a gas (aerogel), liquid (gel) or solid (dispersed or co-continuous). The emphasis of this discussion is on reversible networks. They require a reversing stimulus, typically heat, shear, pH, electrical or magnetic. The magnitude of the reversing force is important for application. Thermoplastic rubbers require reversal of physical cross-links during processing, for all other circumstances they must have a permanent network structure. Reological additives exhibit network reversal on shear and the gelling forces should be weak and potentially rapidly reversible. Dispersive forces, called hydrophobic forces when a polar medium is the matrix, meet networking criteria. Ionic or dipolar forces can be enhanced by molecular orientation formed by shear or an electrical field thus causing an increase in structure formation with a rheopectic or shear thickening effect. In solids such additives modify the viscoelastic properties. The distinction between a liquid and a solid is uncertain for amorphous materials. A feature of more recent research is the formation of self-assembling network systems, often using functionalized polymers with interacting groups having high specificity and facile reversibility. Reversibility is either self-controlled in response to changes in the environment or activated by external stimuli, such as those mentioned above. Materials with these responsive changes to their structure have been called smart materials. A reverse situation may apply where changes in the structure of the material lead to changes in the stimulus field. Changing chemical, mechanical or shear conditions may lead to a change in conductivity or light transmission, so the material can become a sensor. Nematic liquid crystalline ordering of side-chain mesogens can be controlled by electro-optical stimuli. Thermo-reversible networks are much studied, but network formation can be activated by electrical or magnetic fields. Many new materials are based upon the principles that have been discussed with the similarity that they include reversible supramolecular structures.

Supramolecular surface-confined architectures created by self-assembly of triangular phenylene–ethynylene macrocycles via van der Waals interaction

At the liquid/graphite interface triangular and rhombic phenylene-ethynylene macrocycles substituted by alkyl chains self-assemble to form porous two-dimensional (2D) molecular networks of honeycomb and Kagomé types, respectively, or close-packed non-porous structures via alkyl chain interdigitation as the directional intermolecular linkages. Factors that affect the formation of the 2D molecular networks, such as alkyl chain length, solvent, solute concentration, and co-adsorption of guest molecules, were elucidated through a systematic study. For the porous networks, various molecules and molecular clusters were adsorbed in the pores reflecting the size and shape complementarity, exploring a new field of 2D host-guest chemistry.

Passing Current through Touching Molecules

The charge flow from a single C(60) molecule to another one has been probed. The conformation and electronic states of both molecules on the contacting electrodes have been characterized using a cryogenic scanning tunneling microscope. While the contact conductance of a single molecule between two Cu electrodes can vary up to a factor of 3 depending on electrode geometry, the conductance of the C(60)-C(60) contact is consistently lower by 2 orders of magnitude. First-principles transport calculations reproduce the experimental results, allow a determination of the actual C(60)-C(60) distances, and identify the essential role of the intermolecular link in bi- and trimolecular chains.

The elementary softening event in glassy systems in terms of the model of the excited state

The pressure dependence of the glass-transition temperature (glass-transition lines) is described through a relationship similar to the Clausius-Clapeyron equation. The criterion for the glass-liquid transition for polymer and other glasses is calculated. According to the proposed speculations, an elementary softening event in glasses is reduced to the critical deformation of interatomic (intermolecular) linkage, which corresponds to the maximum force of attraction between atoms. A glass (an amorphous polymer) softens when the mean energy of the thermal motion of the kinetic units responsible for the viscous flow is ∼3 times higher than the work of the ultimate deformation of the interatomic bond. The nature of structural changes occurring in the course of critical displacement (excitation) of kinetic units in liquids and glasses is discussed.

Supramolecular association of 1,2,5-chalcogenadiazoles: an unexpected self-assembled dissymetric [Se⋯N]2 four-membered ring

The structure of a self-assembled system containing benzoselenadiazole with the corresponding cationic N-methyl salt was determined by X-ray diffraction analysis. The assembly has a distinct tendency to establish intermolecular links in the solid state through secondary intermolecular bonding Se⋯N interactions. In such supramolecular association, the observation of an unusual asymmetric four-member ring [Se⋯N]2 with a short contact of 2.573 A and a long contact of 2.966 A was observed.

Thiophene-2-carbaldehyde 2,4-dinitrophenylhydrazone

In the approximately planar molecule of the title compound, C11H8N4O4S, the dihedral angle between the thio­phene and benzene rings is 5.73 (10)°. In the crystal structure, bifurcated inter/intra­molecular N—H⋯(O,O) hydrogen bonds are present. The intermolecular links lead to inversion dimers containing an R 2 2(12) graph-set motif.

Fragmentations of (M–H)− anions of underivatised peptides. Part 2: Characteristic cleavages of Ser and Cys and of disulfides and other post‐translational modifications, together with some unusual internal processes

In a previous review (Bowie, Brinkworth, & Dua (2002); Mass Spectrom Rev 21:87-107) we described the characteristic backbone cleavages and side chain fragmentations which occur from (M-H)(-) parent anions of underivatized peptides. This work is briefly summarized in the present review. Cys was not described in the previous review: here we describe the Cys characteristic side chain loss of H(2)S, together with its gamma backbone cleavage. These processes are compared with those of the related Ser. All experimental observations are backed up with theoretical studies at the HF/6-31G(d)//AM1 level of theory, a level of theory which we have shown gives good geometries and acceptable relative energies. The negative ion cleavages of a number of post-translational modifications are described. Negative ion mass spectrometry is the method of choice for identification of disulfides in both peptides and proteins. Intramolecular disulfides are identified by the presence of the fragment anion [(M-H)(-)-H(2)S(2)], and CID MS2 of this fragment normally identifies the positions of the two Cys residues and often the full sequence of the peptide. An unsymmetrically substituted intermolecular disulfide can give up to eight characteristic fragment anions, and CID MS2 of some, or all of these often provides the full sequence of those peptides which form the initial intermolecular disulfide linkage. Negative ion cleavages of disulfides are the most energetically favored of all peptide negative cleavages studied to date. Negative ion mass spectrometry is also valuable for the identification of pyroglutamates, sulfates and phosphates. Finally, some unusual fragmentations are described which involve cyclization/elimination reactions which require the decomposing (M-H)(-) parent anions to adopt the same helical conformation that these peptides have in solution.

Partial oxidation and oxidative polymerization of metallothionein

One mechanism for regulation of metal binding to metallothionein (MT) involves the non-enzymatic or enzymatic oxidation of its thiols to disulfides. Formation and speciation of oxidized MT have not been investigated in detail despite the biological significance of this redox biochemistry. While metal ion-bound thiols in MT are rather resistant towards oxidation, free thiols are readily oxidized. MT can be partially oxidized to a state in which some of its thiols remain reduced and bound to metal ions. Analysis of the oxidation products with SDS-PAGE and a thiol-specific labeling technique, employing eosin-5-iodoacetamide, demonstrates higher-order aggregates of MT with intermolecular disulfide linkages. The polymerization follows either non-enzymatic or enzymatic oxidation, indicating that it is a general property of oxidized MT. Supramolecular assemblies of MT add new perspectives to the complex redox and metal equilibria of this protein.

Mapping Disulfide Bonds in Insulin with the Route 66 Method: Selective Cleavage of S [sbnd]C Bonds Using Alkali and Alkaline Earth Metal Enolate Complexes

Simple and fast identification of disulfide linkages in insulin is demonstrated with a peptic digest using the Route 66 method. This is accomplished by collisional activation of singly and doubly charged cationic Na(+) and Ca(2+) complexes generated using electrospray ionization mass spectrometry (ESI-MS). Collisional activation of doubly charged metal complexes of peptides with intermolecular disulfide linkages yields two sets of singly charged paired products separated by 66 mass units resulting from selective SC bond cleavages. Highly selective elimination of 66 mass units, which corresponds to the molecular weight of hydrogen disulfide (H(2)S(2)), is observed from singly charged metal complexes of peptides with disulfide linkages. The mechanism proposed for these processes is initiated by formation of a metal-stabilized enolate at Cys, followed by cleavage of the S-C bond. Further activation of the products yields sequence information that facilitates locating the position of the disulfide linkages in the peptic digest fragments. For example, the doubly charged Ca(2+) complex of the peptic digest product GIVEQCCASVCSL/FVNQHLCGSHL yields paired products separated by 66 mass units resulting from selective SC bond cleavages at an intermolecular disulfide linkage under low-energy collision-induced dissociation. Further activation of the product comprising the A chain reveals the presence of a second disulfide bridge, an intramolecular linkage. Experimental and theoretical studies of the disulfide linked model peptides provide mechanistic details for the selective cleavage of the S-C bond.

Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization

Repeating intermolecular protein association by means of beta-sheet expansion is the mechanism underlying a multitude of diseases including Alzheimer's, Huntington's and Parkinson's and the prion encephalopathies. A family of proteins, known as the serpins, also forms large stable multimers by ordered beta-sheet linkages leading to intracellular accretion and disease. These 'serpinopathies' include early-onset dementia caused by mutations in neuroserpin, liver cirrhosis and emphysema caused by mutations in alpha(1)-antitrypsin (alpha(1)AT), and thrombosis caused by mutations in antithrombin. Serpin structure and function are quite well understood, and the family has therefore become a model system for understanding the beta-sheet expansion disorders collectively known as the conformational diseases. To develop strategies to prevent and reverse these disorders, it is necessary to determine the structural basis of the intermolecular linkage and of the pathogenic monomeric state. Here we report the crystallographic structure of a stable serpin dimer which reveals a domain swap of more than 50 residues, including two long antiparallel beta-strands inserting in the centre of the principal beta-sheet of the neighbouring monomer. This structure explains the extreme stability of serpin polymers, the molecular basis of their rapid propagation, and provides critical new insights into the structural changes which initiate irreversible beta-sheet expansion.

Formation of cytotoxic transthyretin is not dependent on inter-molecular disulphide bridges commonly found within the amyloid form

Familial amyloidotic polyneuropathy (FAP) is linked to destabilising point mutations in the human plasma protein transthyretin (TTR). Consistent with similar amyloid disorders, low molecular weight TTR oligomers have been shown to exert the major cytotoxic effect. The amyloid structure of TTR contains non-native inter-molecular disulphide linkages via the cysteine at position 10 (Cys10). Moreover, substitution of Cys10 in a mouse model for TTR-amyloidosis abolishes TTR deposits, indicating an important role of Cys10 in FAP pathogenesis. However, the role of disulphide bridges in TTR cytotoxicity has not been elucidated. By probing Cys10Ser TTR variants to the human neuroblastoma SH-SY5Y cell line, we have addressed this question, and our results clearly show that formation of an inter-molecular disulphide bridge is not a pre-requisite for TTR cytotoxicity. This finding suggests that prevention of inter-molecular TTR disulphide bridges as a therapeutic intervention will not impair the cytotoxic potential of TTR.

Molecular basis of the redox regulation of SUMO proteases: a protective mechanism of intermolecular disulfide linkage against irreversible sulfhydryl oxidation

Sumoylation has emerged as an indispensable post-translational modification that modulates the functions of a broad spectrum of proteins. Recent studies have demonstrated that reactive oxygen species influence the equilibrium of sumoylation-desumoylation. We show herein that H2O2 induces formation of an intermolecular disulfide linkage of human SUMO protease SENP1 via the active-site Cys 603 and a unique residue Cys 613. Such reversible modification confers a higher recovery of enzyme activity, which is also observed in yeast Ulp1, but not in human SENP2, suggesting its protective role against irreversible sulfhydryl oxidation. In vivo formation of a disulfide-linked dimer of SENP1 is also detected in cultured cells in response to oxidative stress. The modifications are further elucidated by the crystal structures of Ulp1 with the catalytic cysteine oxidized to sulfenic, sulfinic, and sulfonic acids. Our findings suggest that, in addition to SUMO conjugating enzymes, SUMO proteases may act as redox sensors and effectors modulating the desumoylation pathway and specific cellular responses to oxidative stress.

Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts

Disulfide bonds play an important role in protein stability and function. Here, we describe a general procedure for generating disulfide-linked dimers and multimers of proteins of known crystal structures. An algorithm was developed to predict sites in a protein compatible with intermolecular disulfide formation with neighboring molecules in the crystal lattice. A database analysis was carried out on 46 PDB coordinates to verify the general applicability of this algorithm to predict intermolecular disulfide linkages. On the basis of the predictions from this algorithm, mutants were constructed and characterized for a model protein, thioredoxin. Of the five mutants, as predicted, in solution four formed disulfide-linked dimers while one formed polymers. Thermal and chemical denaturation studies on these mutant thioredoxins showed that three of the four dimeric mutants had similar stability to wild-type thioredoxin while one had lower stability. Three of the mutant dimers crystallized readily (in four to seven days) in contrast to the wild-type protein, which is particularly difficult to crystallize and takes more than a month to form diffraction-quality crystals. In two of the three cases, the structure of the dimer was exactly as predicted by the algorithm, while in the third case the relative orientation of the monomers in the dimer was different from the predicted one. This methodology can be used to enhance protein crystallizability, modulate the oligomerization state and to produce linear chains or ordered three-dimensional protein arrays.