Contribution of tyrosine to circular dichroism changes accompanying neurophysin-hormone interaction

Measuring Structural Changes in Cytochrome c under Crowded Conditions Using In Vitro and In Silico Approaches

It is known from in vitro studies that macromolecular crowding in the cell effects protein structure, stability and function; but predictive studies are relatively unexplored. There are few reports where the effect of various crowder mixtures has been exploited to discern their combined effect on the structural stability of proteins. These studies are more significant because their effect can mimicked with in vivo conditions, where the environment is heterogeneous. Effects of two crowders, polyethylene glycol (PEG 400 Da), and its monomer ethylene glycol (EG) alone and in mixture on the structural stability of cytochrome c (cyt c) were determined using various spectroscopic and bioinformatics tools. The main conclusions of our study are (i) the monomer EG has a kosmotropic effect on the protein (stabilizes the protein), and has no significant effect on the tertiary structure; (ii) PEG 400 destabilizes the structure as well as the stability of the protein; and (iii) EG counteracts the destabilizing effect of PEG 400. From this investigation, it seems evident that proteins may fold or unfold in the crowded environment of the cell where various interactions assist them to maintain their structure for their functions. Bioinformatics approaches were also used to support all of the in vitro observations. Cyt c is functional protein; if the structure of the protein is modulated due to change in the environment its nature of function will also change. Our research addresses the question by modulating the environment around the protein, and the macromolecule (protein) conformation dynamics and interaction study via in vitro and in silico approaches which indirectly compares with that of the environment in-cellular milieu, which is highly crowded.

Interaction of polyethylene glycol with cytochrome c investigated via in vitro and in silico approaches

One of the significant proteins that have attracted research groups due to virtue of being a potent selective anticancer drug target and property of triggering apoptosis upon release in cytoplasm is cytochrome c (cyt c). The mechanical transformations due to the macromolecular crowding in membrane in the mammalian cell are proposed to be useful inductors of changes in volume. It is very interesting to know that mitochondrial function were observed to be improved by polyethylene glycol (PEG) interaction, which in turn inhibits the cyt c (a pro-apoptotic cell death factor). In this work, the effect of polyethylene glycol of molecular weight 4 kilo Dalton (PEG 4 kDa) was investigated to highlight the structural transformations (tertiary and secondary structure) in cyt c using a choice of spectroscopic techniques (including UV-Vis absorption, near-UV, far-UV and Soret circular dichroism and fluorescence spectroscopy), which shows noteworthy shifts in the secondary and tertiary structures at higher concentrations of PEG 4 kDa with small changes in the heme-globular interactions. The size distribution changes of native protein treated with various concentrations of the crowder were observed and analyzed by dynamic light scattering (DLS). The interaction studies of the crowder with the protein was observed and analyzed by FTIR, isothermal titration calorimetry, time resolved fluorescence and molecular docking. The investigations suggested that the structural changes in the protein occurred due to soft interactions of PEG 4 kDa, which usually destabilizes proteins. The experimental evidence in this study proposed that crowding could be another approach to mechanical super-competition and free of certain markers that could aid in the identification and control of various diseases. This study suggests that crowders at specific concentrations, which softly interact with proteins, can be exploited as remedy for various diseases.

End-group modified retro-inverso isomers of tripeptide oxytocin analogues: binding to neurophysin II and enhancement of its self-association properties

The importance of peptide backbone structure in peptide/protein recognition events has been tested evaluating the binding properties of end-group modified retro-inverso isomers of MYF and LYF amides, tripeptides able to mimic oxytocin in binding neurophysin II and in potentiating its self-association. The isomers, topochemically related to their parent peptides, have been prepared respectively from all-D N-acetyl-FYM and N-acetyl-FYL amides via the Hofmann-type rearrangement mediated by iodobenzene bis-trifluoroacetate. Retro-inverso isomers recognised neurophysin II with similar affinity as the parent peptides, as determined by analytical affinity chromatography on columns prepared immobilising neurophysin II on preactivated supports. In addition, their effect on neurophysin II self-association was similar to the tripeptide oxytocin analogues, potentiating neurophysin II dimerization to the same extent, as evaluated by solid-phase binding assays on microtiter plates coated with neurophysin II. Recognition specificity of retro-inverso isomers was further demonstrated by their inhibitory effect on the interaction between neurophysin II and oxytocin tripeptide analogues. Results suggest that only the proper orientation of the alpha-amino group and of the side chains plays a dominant role in the binding of tripeptide analogues to neurophysin II and potentiation of its self-association, while the peptide backbone topology has little influence on the recognition process.

Amino acid sequence and properties of vasopressin-associated elephant neurophysin

The primary structure of an elephant neurophysin, homologous to vasopressin-associated neurophysins, is reported. The protein contains a Tyr for Asn substitution at position 75, a position in direct contact with residues 77 and 78 of the monomer-monomer interface. This Tyr residue therefore serves as a potential reporter of the path involved in the long-range linkage between peptide binding and dimerization in this system. NMR studies of the protein in unliganded and liganded states demonstrated normal dimerization properties and the expected increase in dimerization associated with binding peptide. In keeping with an elevated pKa of 11.1 assigned to Tyr-75 by UV spectrophotometric titration, the NMR signals from the 3,5 and 2,6 ring protons of Tyr-75 were shifted 0.3 and 0.2 ppm upfield, respectively, relative to their positions in small peptides, indicating significant shielding and/or hydrogen bonding. The Tyr-75 ring proton signals narrowed slightly, with no discernible change in chemical shift, on conversion from dimer to monomer in the unliganded state. Ring protons of Tyr-49, distant from the monomer-monomer interface, but adjacent to the peptide-binding site, were markedly perturbed by dimerization, in accord with their behavior in bovine neurophysins. The results suggest that the secondary and tertiary structure of the region 75-78 is largely unchanged by dimerization, and argue against an important role for this region in dimerization-mediated conformational changes that alter the binding site in the unliganded state.(ABSTRACT TRUNCATED AT 250 WORDS)

The conformation of deamino-oxytocin: X-ray analysis of the 'dry' and 'wet' forms

Two crystal structures of (1 beta-mercaptopropionic acid) deamino-oxytocin are reported. The 'dry form' in space group C2 has cell dimensions a = 27.08 +/- 0.03, b = 9.06 +/- 0.01, c = 22.98 +/- 0.02 A, beta = 102.06 +/- 0.03 with one deamino-oxytocin and six water molecules per asymmetric unit. The 'wet form' in space group P2(1) has cell dimensions a = 27.27 +/- 0.02, b = 9.04 +/- 0.01, c = 23.04 +/- 0.02 A, beta = 102.24 +/- 0.02, with two deamino-oxytocin and 13 water molecules per asymmetric unit. A local twofold parallel to the monoclinic axis gives a pseudo C2 packing. Initial phases of the 'dry form' were calculated by the heavy-atom method from the isomorphous and anomalous difference Pattersons and anomalous difference Fouier synthesis. The structure was refined by using restrained least-squares at 1.2 A resolution to a crystallographic R = 0.10. The molecular replacement method yielded the P2(1) structure that was refined with geometric restraints to R less than 0.09, by using all data to 1.09 A resolution. Deamino-oxytocin consists of a cyclic tocin ring formed by six amino acids, closed by a disulphide bridge, S1-S6, and held by two trans-annular hydrogen bonds N2-O5 and N5-O2 with a type II turn at residues 3 and 4. A flexible tripeptide tail has a loosely hydrogen-bonded type I beta-turn between N9 and O6. The sulphur of cysteine at position 1 is disordered in all the molecules leading to alternative hands of disulphide. The conformational flexibility of Ile 3, Asn 5, Pro 7 side chains and the disulphide bridge is consistent with previous models of oxytocin in which flexibility is necessary for biological activity.

Influence of neurophysin residues 1-8 on the optical activity of neurophysin-peptide complexes. Direct evidence that the 1-8 sequence alters the environment of bound peptide

Circular dichroism was used to compare the environment of peptides bound to native and des 1-8 neurophysin in order to further elucidate the role of the neurophysin 1-8 sequence in peptide-binding. A very large positive ellipticity (approximately 6000 deg cm2 dmol-1), shown earlier to be induced in tyrosine at position 2 of peptides bound to the native protein, was determined by the present study to be paralleled by similar induced changes in tyrosine at peptide position 1. Deletion of the neurophysin 1-8 sequence led to loss of half of the induced optical activity at peptide positions 1 and 2 and changes in binding-induced optical activity in the protein, the latter partially assignable to protein disulfides. In the mononitrated native and des 1-8 proteins, the optical activity of neurophysin Tyr-49, a residue at the peptide-binding site, was reduced by 80% in complexes of the des 1-8 protein relative to those of the native protein. The results suggest a role for neurophysin Arg-8 in modulating the optical activity at the binding site by directly placing a charge proximal to the binding site and/or by altering binding site conformation. The data provide the first unambiguous evidence of a difference in the environment of bound peptide between the native and des 1-8 proteins.

A semisynthetic bovine pancreatic ribonuclease containing a unique nitrotyrosine residue

A fully active semisynthetic ribonuclease, RNase 1-118:111-124, may be prepared by enzymatically removing six residues from the COOH terminus of the protein (positions 119-124) and then complementing the inactive RNase 1-118 with a chemically synthesized peptide containing the COOH-terminal 14 residues of the molecule (RNase 111-124) [M. C. Lin, B. Gutte, S. Moore, and R. B. Merrifield (1970) J. Biol. Chem. 245, 5169-5170]. Nitration of tyrosine-115 in the peptide followed by complex formation with RNase 1-118 affords a fully active enzyme containing a unique nitrotyrosine residue in a position which is known and which is very likely to be completely exterior to the active site region. The binding constant between the tetradecapeptide and RNase 1-118 (5 X 10(6) M-1 at pH 6.0) is not changed by the nitration. Crystals of the nitrated complex are isomorphous with those of RNase 1-118:111-124, for which a refined 1.8-A structure has recently been obtained.

Enthalpies of ligand binding to bovine neurophysins

Flow microcalorimetry and batch microcalorimetry have been used to survey the energetics of ligand binding by bovine neurophysins I and II. Calorimetry studies were supplemented by van't Hoff analyses of binding constants determined by circular dichroism. Free energies of binding of a series of di- and tripeptides that bind to the strong hormone binding site of neurophysin were partitioned into their enthalpic and entropic components. The results indicate that, at 25 degrees C, the binding of most peptides is an enthalpy-driven reaction associated with negative entropy and heat capacity changes. Studies elsewhere, supported by evidence here, indicate that the principal component of the negative enthalpy change does not arise from the increase in neurophysin dimerization associated with peptide binding. Accordingly, the negative enthalpy change is attributed to direct bonding interactions with peptide and possibly also to peptide-induced changes in tertiary or quaternary organization. Comparison of the binding enthalpies of different peptides indicated two types of bonding interactions that contribute to the negative enthalpy change of peptide ligation. Substitution of an aromatic- or sulfur-containing side chain for an aliphatic side chain in position 1 of bound peptides led to increases in negative enthalpy of from 1 to 6 kcal/mol, demonstrating that interactions typically classified as hydrophobic can have a significant exothermic component at 25 degrees C. Similarly, loss of hydrogen bonding potential in the peptide decreased the enthalpy change upon binding, in keeping with the expected enthalpic contribution of hydrogen bonds. In particular, the data suggested that the peptide backbone between residues 2 and 3 and the phenolic hydroxyl group in position 2 participate in hydrogen bonding.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural and circular-dichroism studies on the interaction between human C1-esterase inhibitor and C1s

The reaction between complement factor C1s and C1-esterase inhibitor has been investigated by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis, N-terminal amino acid analysis and c.d. studies. It is confirmed that a very stable stoichiometric 1:1 complex with a molecular weight of about 180000 is formed, involving the light chain of C1s. On the sodium dodecyl sulphate/polyacrylamide gels a small peptide with a molecular weight of about 5000 can be seen, which may be released from the C-terminal portion of the inhibitor moiety in a manner analogous to that occurring in other similar proteinase-inhibitor reactions. By N-terminal amino acid analysis, a newly formed threonine residue is found in the complex, suggesting that the inhibitor peptide chain is cleaved in the complex between C1s and C1-esterase inhibitor. The stabilizing bond may therefore be an ester bond. C.d. studies of the native C1-esterase inhibitor indicated the presence of about 38% alpha-helix, about 24% beta-structure and about 38% unordered structure. By gradual cleavage of the disulphide bridges under non-denaturating conditions, gradual changes in the c.d. spectra occurred, suggesting loss of ordered secondary structures. The c.d. spectra of the complex between C1s and C1-esterase inhibitor indicate that tryptophan residues are affected by the complex-formation.

Binding of neurohypophyseal peptides to neurophysin dimer promotes formation of compact and spherical complexes

Previous hydrodynamic studies [Rholam, M., & Nicolas, P. (1981) Biochemistry 20, 5837-5843] have demonstrated that the dimerization of a neurophysin monomer (prolate ellipsoid with an axial ratio, due to asymmetry, of 5.2) results in a decreased asymmetry (axial ratio, due to asymmetry, of 3.6) as the consequence of a side-by-side association process. By a combination of hydrodynamic measurements, including the use of sedimentation velocity, viscometry, and fluorescence polarization spectroscopy, the influence of hormone binding on the shape and asymmetry properties of the neurophysin dimer was evaluated. The binding of ocytocin, vasopressin, and the tripeptide analogue of the N-terminal sequence of ocytocin, Cys(S-Me)-Tyr-Ile-NH2, results in an increase of S020,W and a decrease in both the reduced viscosity and rotational relaxation time of the bis-liganded dimeric species vs. the nonliganded form. The axial ratio (a/b) due to asymmetry of the ligand-bound dimers was found in each case to be equal to, or slightly greater than, 1.0, indicating a compact spherical shape (Stokes radius 21 A). The profound alteration on molecular dimensions observed upon ligand binding is shown to be the consequence of a ligand-induced conformational change and might explain the intradimeric binding sites positive cooperativity. It is tentatively proposed that the pseudospherical shape of the neurophysin-hormone complexes may enhance the stability of neurophysin and contribute to the prevention of leakage of neuropeptides through the membrane of neurosecretory granules. The data provide a remarkable example of a small protein with a high content in disulfide links and that undergoes conspicuous changes in conformation under the influence of nonapeptide, or tripeptide, ligands.

Synthesis of peptide spin-labels that bind to neurophysin and their application to distance measurements within neurophysin complexes

The synthesis of two spin-labels capable of binding to the hormone-binding site(s) of neurophysin is described. The two spin-labels are 4-(glycyl-L-phenylalanylamido)-2,2,6,6-tetramethylpiperidinyl-1-oxy and S-[[[3-(2,2,5,5-tetramethylpyrrolidine-1-oxy)amino]carbonyl]methyl]-L-cysteinyl -L-tyrosine amide; synthesis of the former is achieved by a novel route to circumvent problems associated with nitroxide instability under standard conditions of peptide deblocking. NMR studies of the effects of binding these spin-labels on relaxation rates of individual proton resonances of neurophysin were used to calculate correlation times and distances between the bound nitroxides and the observed protons. The results indicate that residue 3 of peptides bound to the strong site of neurophysin is greater than or equal to 14 A from Tyr-49 and argue against a distance of < 5 A between the ortho ring protons of Tyr-49 and those of residue 2 of peptides bound to the strong site. Alternatively, the data suggest that the previously observed nuclear Overhauser effect between these protons reflects spin diffusion at the strong site and a contribution of uncertain magnitude from a second but very weak binding site; this second site is close to Tyr-49 and is detected by the increased relaxation rate of Tyr-49 ring protons when 4-(glycyl-L-phenylalanylamido)-2,2,6,6-tetramethylpiperidinyl-1-oxy is displaced from the strong site by competing diamagnetic peptide. Additionally, the data indicate that residue 3 of bound peptides at the strong site is distant from His-80 but approximately 12 A from the amino terminus. The extended side chain of residue 1 of peptides at the strong site is calculated as less than or equal to 10 A from Tyr-49.

Stopped-flow investigation of nitrated bovine neurophysin monomer binding to oxytocin

By use of stopped-flow kinetic data, we have measured the kinetics of mononitrated neurophysin I monomer binding to oxytocin. The association constant was 1.3(+/-0.3) x 10(5) M-1s-1 and the dissociation rate constant was 2.0(+/-0.5)s-1 for protonated oxytocin binding. Both rates are significantly slower than those observed for neurophysin dimer. These data suggest that the binding process by which the monomer binds oxytocin is not identical to that of dimer.

Circular dichroism spectra of cleavage fragments of soybean trypsin-chymotrypsin inhibitor

Circular dichroism spectra of biologically active fragments of Bowman-Birk soybean inhibitor have been determined in acidic, neutral, and alkaline conditions. Neither fragment showed evidence of alpha-helix or beta-structure. Negative dichroism above 260nm has been assigned in both fragments primarily to disulfide bonds, with a minor contribution from tyrosine in a hydrophilic environment. The individual spectra of these fragments, and their sum between 230 and 340 nm have been compared with the spectra of the intact inhibitor and several structurally related proteins. Possible interactions which may give rise to CD bands in this region are discussed.

Circular dichroism spectra of isolated soybean and chickpea trypsin-chymotrypsin inhibitors

Circular dichroism spectra of trypsin-chymotrypsin inhibitors from soybeans and chickpeas have been determined in acidic, neutral and highly alkaline solutions. Neither protein contains alpha-helix although a small amount of beta-structure cannot be excluded. Negative dichroism above 250 nm has been assigned largely to disulfide bonds in both molecules with neither showing evidence for tyrosine residues buried in hydrophobic regions. The spectra of these inhibitors between 230 and 250 nm have been compared with the spectra of a number of structurally related proteins suggesting that previous interpretations of this region may have been incomplete or incorrect.

Drug-biomolecule interactions: proton magnetic resonance studies of complex formation between bovine neurophysins and oxytocin at molecular level

Proton magnetic resonance spectroscopy was used to monitor individual amino acid residues in bovine neurophysin, in the nonapeptide hormone oxytocin, and in the complex formed between them. For neurophysin I alone, a normal titration curve for the C-2 proton resonance of the lone histidine residue was obtained with an apparent ionization constant of 6.9 addition of oxytocin to a solution of neurophysin I at pH 6.5 resulted in several changes in the spectrum. The effect on the histidine C-2 proton resonance signal indicated a slow exchange process between two states, probably representing a conformational change in the protein. The apparent pK of the histidine residue in the hormonal complex was shifted to 6.7, indicating a slightly more positive (less electron dense) environment for the histidine residue. Resonances of the single tyrosine residue of oxytocin were observed to broaden significantly, but not to shift appreciably, on the addition of neurophysin II. These observations may indicate involvement of the tyrosyl residue of oxytocin in the hormone-"carrier protein" interaction.

(2-(3-Nitrotyrosine))oxytocin, a wealky activity analogue of the hormone bound by neurophysin

An analogue of oxytocin containing a nitro group ortho to the phenolic hydroxyl group of the tyrosyl residue was prepared by nitration of the hormone with tetranitromethane. [2-(3-Nitro-l-tyrosine)]oxytocin was bound by neurophysin although its pharmacological activity was virtually abolished. The oxytocic activity of the analogue on the isolated rat uterus was 1.1i.u./mg.