Model-building of neurohypophyseal hormones

From esoteric theory to therapeutic antibodies

Theoretical analyses of amino acid and nucleotide sequences of immunoglobulins have provided a unique approach to the understanding of structure and function of antibodies. Variability plots unambiguously identified that the antibody-combining site is formed by six short complementarity determining regions (CDRs), three each from light and heavy chains. Since three-dimensional (3-D) foldings of framework regions (FRs) are similar among different antibodies, the 3-D configurations of CDRs from a specific antibody can be predicted based on their amino acid sequences. The resulting structure forms a compact surface that fits the antigen molecule tightly. The third CDR of the heavy chain (CDRH3), which is coded by the D-minigene together with the N- and/or P-segments, appears to play a unique role in fine fitting between antibody and antigen molecules. In order to maintain biological activities, the grafting of mouse CDRs onto human FRs should closely match the human FR amino acid sequences with the original mouse antibody. Similarities between human and mouse FR sequences that have been preserved for over 20 million years of evolution can be a useful tool in humanizing mouse antibodies.

Mechanism of acyl transfer by the class A serine beta-lactamase of Streptomyces albus G

Optimization by energy minimization of stable complexes occurring along the pathway of hydrolysis of benzylpenicillin and cephalosporin C by the Streptomyces albus G beta-lactamase has highlighted a proton shuttle that may explain the catalytic mechanism of the beta-lactamases of class A. Five residues, S70, S130, N132, T235 and A237, are involved in ligand binding. The gamma-OH group of T235 and, in the case of benzylpenicillin, the gamma-OH group of S130 interact with the carboxylate group, on one side of the ligand molecule. The side-chain NH2 group of N132 and the carbonyl backbone of A237 interact with the exocyclic CONH amide bond, on the other side of the ligand. The backbone NH groups of S70 and A237 polarize the carbonyl group of the scissile beta-lactam amide bond. Four residues, S70, K73, S130 and E166, and two water molecules, W1 and W2, perform hydrolysis of the bound beta-lactam compound. E166, via W1, abstracts the proton from the gamma-OH group of S70. While losing its proton, the O-gamma atom of S70 attacks the carbonyl carbon atom of the beta-lactam ring and, concomitantly, the proton is delivered back to the adjacent nitrogen atom via W2, K73 and S130, thus achieving formation of the acyl-enzyme. Subsequently, E166 abstracts a proton from W1. While losing its proton, W1 attacks the carbonyl carbon atom of the S70 ester-linked acyl-enzyme and, concomitantly, re-entry of a water molecule W'1 replacing W1 allows E166 to deliver the proton back to the same carbonyl carbon atom, thus achieving hydrolysis of the beta-lactam compound and enzyme recovery. The model well explains the differences found in the kcat. values for hydrolysis of benzylpenicillin and cephalosporin C by the Streptomyces albus G beta-lactamase. It also explains the effects caused by site-directed mutagenesis of the Bacillus cereus beta-lactamase I [Gibson, Christensen & Waley (1990) Biochem J. 272, 613-619].

Dynamics and conformational energetics of a peptide hormone: vasopressin

A theoretical methodology for use in conjunction with experiment was applied to the neurohypophyseal hormone lysine vasopressin for elucidation of its accessible molecular conformations and associated flexibility, conformational transitions, and dynamics. Molecular dynamics and energy minimization techniques make possible a description of the conformational properties of a peptide in terms of the precise positions of atoms, their fluctuations in time, and the interatomic forces acting on them. Analysis of the dynamic trajectory of lysine vasopressin shows the ability of a flexible peptide hormone to undergo spontaneous conformational transitions. The excursions of an individual phenylalanine residue exemplify the dynamic flexibility and multiple conformational states available to small peptide hormones and their component residues, even within constraints imposed by a cyclic hexapeptide ring.

Biofunctional evaluation of a hydrogen bond stabilizing the conformation in the cyclic part of oxytocin

[5-beta-Malamidic acid]oxytocin was synthesized to study the importance of the hydrogen bond between the C=O of Tyr2 and the peptide N-H of Asn5 for the stabilization of a biologically functional conformation of oxytocin. This analog lacks the peptide N-H at residue 5 required for the formation of a hydrogen bond with the C-O of Tyr2. [5-beta-Malamidic acid] oxytocin exhibited 45.1 +/- 2.5 U/mg and 65.6 +/- 5.9 U/mg of uterotonic activity, in vitro, in the absence and in the presence, respectively, of Mg2+, 147 +/- 14 U/mg of uterotonic activity in vivo, 203 +/- 13 U/mg of milk-ejecting activity, 0.37 +/- 0.03 U/mg of pressor activity and 0.32 +/- 0.29 U/mg of antidiuretic activity. It is concluded that devoid of the hydrogen bond under question, an oxytocin-like peptide can still assume the conformation needed to interact with the oxytocin receptors.

H N.M.R. study of the conformation of [Glu4] oxytocin and its lanthanide complexes in aqueous solution

At 400 MHz the 1H chemical shifts, peptide NH-C alpha H coupling constants (JN alpha) and peptide hydrogen exchange rates of [Glu4] oxytocin in aqueous solution closely resemble those previously reported for oxytocin under comparable conditions, indicating that both the parent hormone and its analogue have similar conformations in this solvent. The hydrogen exchange data suggest a dynamic equilibrium between conformation(s) in which the peptide NH's of Asn5 and Cys6 are internally hydrogen bonded and conformation(s) in which these hydrogens are bonded to the solvent. [Glu4] oxytocin forms 1:1 complexes with lanthanide metal ions. The diamagnetic La3+ complex exhibits values of JN alpha very similar to those of the metal free hormone analogue, suggesting that coordination of the metal is accompanied by minimal perturbation of the peptide backbone. Specific average proton-metal distances estimated from Gd3+ induced paramagnetic relaxation effects indicate that the metal is probably coordinated to the Glu4 carboxyl group and the sidechain carbonyl of Asn5. Limiting shifts induced by binding of paramagnetic Yb3+ are also reported.

Intramolecularly hydrogen-bonded peptide conformations

Over the past few years the possible occurrence of intramolecularly hydrogen-bonded structures in linear and cyclic peptides has attracted increasing attention. In this review emphasis is given to solid-state studies, particularly by X-ray diffraction and infrared absorption techniques. Conformational energy calculations are also considered. The discussion is focused both on model peptides and biological activity polypeptide molecules. The tetrapeptide system (Formula: see text), examined allows one to discuss the extended C5 structure and the various folded conformations, namely the C7 (gamma-turn), C8, C10 (beta-turn), C11, and C13 conformations. The four latter forms may include cis peptide configurations. The oxy-analogs to the C7, C10, and C13 conformations and structures containing bifurcated hydrogen bonds are also discussed. The last sections describe intramolecularly hydrogen-bonded peptide structures involving: (1) a side-chain group, (2) the N-protecting group (in synthetic model compounds), and (3) a beta-amino acid.

Conformational studies of oxytocin analogues with different ring sizes. I. Circular dichroism

Circular dichroic spectra were measured for three analogues of deamino-oxytocin of different ring sizes where the disulfide group of oxytocin is replaced by the (CH2)n group. Their backbone rings are composed of different numbers of atoms, i.e., they are nineteen, twenty and twenty-one for [1,6-aminopimelic acid]oxytocin (n = 1), [1,6-aminosuberic acid]oxytocin (n = 2) and [1,6-aminoazelaic acid]oxytocin (n = 3), respectively. The pH dependence of the circular dichroism spectra indicates that the conformation of [1,6-aminoazelaic acid]oxytocin is different from those of others and the temperature dependency reveals that the conformation of [1,6-aminopimelic acid]oxytocin is most rigid. [1,6-Aminosuberic acid]oxytocin is biologically most active among three derivatives and their biological activities are related to the conformation and internal motions of the peptide hormone analogues.

Theoretical conformational analysis of oxytocin molecule

The total semi-empirical conformational analysis of the oxytocin molecule has been carried out. It has been revealed the two main types of stable structures of cyclic moiety backbone and the great lability of the tail. The optimal spacing of cyclic moiety side chains has been found for every backbone structure. The calculation results are in good agreement with the data of physico-chemical investigations. Among the set of stable molecule structures reported in the present study are structures with beta-turn conformation of the cyclic moiety backbone and without closer spacing of the cyclic moiety and the tail, as well as structures with closely spaced N- and C-terminal parts which, however, lack beta-turn in the cyclic moiety.

Conformation of oxytocin studied by laser Raman spectroscopy

The peptide backbone conformation and salient structural details of oxytocin were examined by laser Raman spectroscopy. Spectra were obtained in the solid phase, water, 2H2O, and dimethyl sulfoxide solutions. A distinct Amide I band was obtained at 1663 cm-1 for aqueous and deuterated samples and 1666 cm-1 for the solid sample. A relatively high frequency Amide III band at 1260 cm-1 was obtained. It is concluded that these Amide I and III bands arise from the "beta-turn"-like conformation of oxytocin. The tyrosine side chain, according to the I850 cm-1/I830 cm-1 intensity ratio, is exposed to the solvent. The S-S stretching vibration at 512 cm-1 indicates the conformation of C-C-S-S-C-C in the disulfide bridge of oxytocin in the ring is gauche-gauche-gauche.

Crystallographic studies of protein denaturation and renaturation. 2. Sodium dodecyl sulfate induced structural changes in triclinic lysozyme

Cross-linked triclinic lysozyme was denatured with sodium dodecyl sulfate. Removal of the denaturant resulted in a refolding of the protein to a conformation similar to but not identical with the native one. Three-dimensional x-ray diffraction data out to 3.2-A resolution were collected for two states in the refolding pathway, and appropriately weighted electron density difference maps were constructed. An analysis of these maps reveals that a sodium dodecyl sulfate molecule is trapped in the interior of the protein, and results in a separation of regions of the polypeptide chain. Our results are discussed in terms of current models for protein folding.

Conformational flexibility and protein folding: rigid structural fragments connected by flexible joints in subtilisin BPN

Conformational energy calculations are used to analyze the interactions of structural substructures in subtilisin BPN. These substructures are kept fixed or "rigid" so that the only variables in the calculations are the backbone segments that separate them. The flexible segments are assumed to be free turns. Using this representation of the protein it is possible to predict both a likely order of events along a folding pathway and preferred modes of conformational changes of the native protein. Moreover, when the native structure has been perturbed by moving the substructures apart, it is possible to assess the range of interactions that return the protein, upon energy minimization, to its original conformation. These results suggest an approach to the folding problem based on the piecemeal formation of tertiary structure from smaller prefolded fragments.

1H nuclear magnetic resonance double resonance study of oxytocin in aqueous solution

Peptide NH resonances in the 250 MHZ 1H nuclear magnetic resonance (NMR) spectrum of oxytocin in H2O were assigned to specific amino acid residues by the "underwater decoupling" technique (i.e., decoupling from corresponding CalphaH resonances, which are buried beneath the intense water peak). These experiments confirm previous assignments of A. I. Brewster an V. J. Hruby ((1973), Proc. Natl. Acad. Sci. U.S.A. 70, 3806) and A. F. Bradbury et al. ((1974), FEBS Lett. 42, 179). Three methods of assigning NH resonances of peptides--solvent titration, underwater decoupling, and isotopic labeling--are compared. As the solvet composition is gradually changed from dimethyl sulfoxide to H2O, oxytocin undergoes a conformational change at 70-90 mol % of H2O. Exposure to solvent of specific hydrogens of oxytocin in H2O was studied by monitoring intensity changes of solute resonances when the solvent peak was saturated. Positive nuclear Overhauser effects (NOE's) of 14 +/- 5 were observed for the Tyr ortho CH and meta CH resonances, respectively. Comparative studies with deamino-oxytocin indicate that these effects result predominantly from intermolecular dipoledipole interaction between aromatic side chain CH protons and protons of the solvent. The NOE's therefore indicate intimate contact between water and the aromatic CH hydrogens of the Tyr side chain. The extent of saturation transferred by proton exchange between water and NH group varies with Ph in a manner which appears to reflect the acid-base catalysis of the protolysis reaction. There is no indication that any NH protons are substantially shiedled from the solvent.

Prediction of the secondary and tertiary structure of plastocyanin

The amino acid sequences of nine plastocyanins were examined using four published methods for the prediction of secondary structure in proteins. The results of the four methods were combined in such a way as to maximize agreement, and the position of alpha helices, beta sheets, and beta turns in plastocyanin was predicted. From this result and other information, such as the position of conserved residues and the requirements for coordination of copper, a preliminary model for the mainchain folding of the molecule was presented.

Conformational studies on arginine vasopressin and arginine vasotocin by proton magnetic resonance spectroscopy

The assignments and partial conformational analysis of the 220-MHz (1)H nuclear magnetic resonance spectrum of the neurohypophyseal hormones arginine vasopressin and arginine vasotocin in uniformaly deuterated dimethylsulfoxide are reported. The chemical shifts, vicinal coupling constants, temperature coefficients of chemical shifts, and proton-deuterium exchange rates for protons of arginine vasopressin and arginine vasotocin are compared with those for the corresponding protons of the related neurohypophyseal hormones lysine vasopressin and oxytocin. Although to a first approximation the backbone conformations of the hormones exhibit conformational similarities, spectral differences are seen for protons in the amino acid residues that comprise the 20-membered ring moieties. It is inferred that there is a gradual shift in the average conformation in going from arginine vasopressin and lysine vasopressin via arginine vasotocin to oxytocin. As judged on the basis of earlier studies, it is evident that the C-terminal acyclic tail moiety exhibits an enhanced mobility over that of the ring moiety in all of the neurohypophyseal hormones studied and, moreover, that this motion is greater in arginine vasopressin and arginine vasotocin than in oxytocin.

Further comparison of predicted and experimentally determined structure of adenylate kinase

An analysis is made of various predictive methods used to locate alpha-helices and beta-sheets in proteins. The analysis is based on attempts to locate the alpha-helices and beta-sheets in adenylate kinase (ATP:AMP phosphotransferase EC 2.7.4.3) from the sequence without prior knowledge of the x-ray findings. Specification of the beta-sheet breaking and alpha-helix breaking tripeptides, a method independent of the others combined with the best of the other methods would substantially reduce the prediction of nonexistent beta-sheets and to a lesser extent would aid in locating alpha-helices.