Model for the three-dimensional structure of vitronectin: predictions for the multi-domain protein from threading and docking

The structure of vitronectin, an adhesive protein that circulates in high concentrations in human plasma, was predicted through a combination of computational methods and experimental approaches. Fold recognition and sequence-structure alignment were performed using the threading program PROSPECT for each of three structural domains, i.e., the N-terminal somatomedin B domain (residues 1-53), the central region that folds into a four-bladed beta-propeller domain (residues 131-342), and the C-terminal heparin-binding domain (residues 347-459). The atomic structure of each domain was generated using MODELLER, based on the alignment obtained from threading. Docking experiments between the central and C-terminal domains were conducted using the program GRAMM, with limits on the degrees of freedom from a known inter-domain disulfide bridge. The docked structure has a large inter-domain contact surface and defines a putative heparin-binding groove at the inter-domain interface. We also docked heparin together with the combined structure of the central and C-terminal domains, using GRAMM. The predictions from the threading and docking experiments are consistent with experimental data on purified plasma vitronectin pertaining to protease sensitivity, ligand-binding sites, and buried cysteines.

Orientation of heparin-binding sites in native vitronectin. Analyses of ligand binding to the primary glycosaminoglycan-binding site indicate that putative secondary sites are not functional

A primary heparin-binding site in vitronectin has been localized to a cluster of cationic residues near the C terminus of the protein. More recently, secondary binding sites have been proposed. In order to investigate whether the binding site originally identified on vitronectin functions as an exclusive and independent heparin-binding domain, solution binding methods have been used in combination with NMR and recombinant approaches to evaluate ligand binding to the primary site. Evaluation of the ionic strength dependence of heparin binding to vitronectin according to classical linkage theory indicates that a single ionic bond is prominent. It had been previously shown that chemical modification of vitronectin using an arginine-reactive probe results in a significant reduction in heparin binding (Gibson, A., Baburaj, K., Day, D. E., Verhamme, I. , Shore, J. D., and Peterson, C. B. (1997) J. Biol. Chem. 272, 5112-5121). The label has now been localized to arginine residues within the cyanogen bromide fragment-(341-380) that contains the primary heparin-binding site on vitronectin. One- and two-dimensional NMR on model peptides based on this primary heparin-binding site indicate that an arginine residue participates in the ionic interaction and that other nonionic interactions may be involved in forming a complex with heparin. A recombinant polypeptide corresponding to the C-terminal 129 amino acids of vitronectin exhibits heparin-binding affinity that is comparable to that of full-length vitronectin and is equally effective at neutralizing heparin anticoagulant activity. Results from this broad experimental approach argue that the behavior of the primary site is sufficient to account for the heparin binding activity of vitronectin and support an exposed orientation for the site in the structure of the native protein.

Charge and solvation effects in anion recognition centers: an inquiry exploiting reactive arginines

Following a long-standing suggestion of Riordan et al. [Riordan, J. F., McElvany, K. D., and Borders, C. L., Jr. (1977) Science 195, 884-885], we sought to exploit chemically activated arginines as probes to characterize the microenvironmental effects in enzymes that mediate the recognition of anionic substrates. A micellar simulation study establishes that octylguanidine (OGn) becomes chemically activated upon incorporation into both cetyltrimethylammonium bromide (CTAB) and Triton X-100 micelles and that the activations correlate with the pKa diminutions induced in its guanidinium group by the effects of electrostatic or nonelectrostatic nature as reflected in the results of pH and salt titration experiments. Next, a protein modification study establishes that the modifiable arginines in a number of enzymes also have diminished pKa's, again due to effects of electrostatic or nonelectrostatic nature as reflected in the results of pH and salt titration experiments. Warwicker's finite difference Poisson--Boltzmann algorithm [Warwicker, J. (1992) J. Mol. Biol. 223, 247-257] is applied to several of the enzymes with available crystal structure coordinates, and indeed, their chemically activated arginines are found to be in an electrostatic microenvironment that can diminish their pKa's, with the magnitudes of these diminutions matching closely the diminutions measured experimentally. Finally, the chemically activated arginines are examined with respect to their atomic atmosphere and are thus found to occur in a local microenvironment that would facilitate their roles as anion anchors. Thus, electrostatic and solvation effects are found to be critical determinants of the arginine role as an anion anchor.

The use of fluorescent probes to characterize conformational changes in the interaction between vitronectin and plasminogen activator inhibitor-1

Plasminogen activator inhibitor-1 (PAI-1), the primary inhibitor of tissue-type plasminogen activator and urokinase, is known to convert readily to a latent form by insertion of the reactive center loop into a central beta-sheet. Interaction with vitronectin stabilizes PAI-1 and decreases the rate of conversion to the latent form, but conformational effects of vitronectin on the reactive center loop of PAI-1 have not been documented. Mutant forms of PAI-1 were designed with a cysteine substitution at either position P1' or P9 of the reactive center loop. Labeling of the unique cysteine with a sulfhydryl-reactive fluorophore provides a probe that is sensitive to vitronectin binding. Results indicate that the scissile P1-P1' bond of PAI-1 is more solvent exposed upon interaction with vitronectin, whereas the N-terminal portion of the reactive loop does not experience a significant change in its environment. These results were complemented by labeling vitronectin with an arginine-specific coumarin probe which compromises heparin binding but does not interfere with PAI-1 binding to the protein. Dissociation constants of approximately 100 nM are calculated for the vitronectin/PAI-1 interaction from titrations using both fluorescent probes. Furthermore, experiments in which PAI-1 failed to compete with heparin for binding to vitronectin argue for separate binding sites for the two ligands on vitronectin.

HOCGO and DMACGO. Two coumarin derived alpha-dicarbonyls suitable as pH and polarity sensitive fluorescent reporters for proteins that can be targeted at reactive arginines

Two coumarin derived alpha-dicarbonyls, HOCGO and DMACGO, are presented as pH, polarity and quencher sensitive fluorescent reporters for proteins that can be targeted at reactive arginines. Both inactivate a number of enzymes that feature functionally critical and chemically susceptible arginyls. Both are chemoselective in responding towards Arg side chain but not towards Cys or Lys side chains under suitably dilute conditions. With pKapp approximately 6.7, HOCGO can serve as a pH sensor, while with pKapp << 4.0, DMACGO is better suited as a polarity sensor. A contrasting set of changes are manifest in the CGOs upon protein interaction that are either attributable to Arg modification or to the noncovalent probe associations with hydrophobic protein domains. DMACGO probes a single hydrophobic site on ovalbumin while HOCGO is largely unresponsive to this protein. Three to five arginyls are modified in HSA and BSA by HOCGO as well as DMACGO, while the latter also probes two hydrophobic sites on both these proteins. HOCGO modifies a single arginine in LDH active site, while its adducts with H4 and M4LDH isozymes titrate to the apparent pKa of 7.8. Other proteins labeled with HOCGO or DMACGO reveal a number of variations that can furnish information about the microenvironment in the sites probed. The CGOs are thus potentially useful reporters of protein domains that feature reactive arginines. Suitable experimental condition are defined based on mechanistic considerations that may be used in applying the CGOs as Arg modifiers and as fluorescent probes.

Exploring borate-activated electron-rich glyoxals as the arginine-reactivity probes. The reactivities of functionally critical arginines in some representative enzymes

4-Substituted styrylglyoxals have been synthesized and found to benefit from borate catalysis to serve as highly reactive arginine modifiers. A study of the mechanism in arginine modification has affirmed: (i) the role of electronic effects in modulating the arginine reactivity in alpha-dicarbonyls, (ii) the intermediacy in the reaction of a reversible arginine-alpha-dicarbonyl complex and (iii) the identity of the nucleophilic attack at ketone as the rate determining step in the arginine reaction with arylglyoxals. 4-Methoxystyrylglyoxal and 4-(N,N-dimethylamino)phenylglyoxal were used as the probes in analyzing some representative enzymes for the reactivities of their susceptible arginyls. The susceptible arginyls in lactate and malate dehydrogenases were thus found to be appreciably reactive while those in carboxypeptidase-A and pyruvate kinase were only moderately reactive.