Volume 8, Issue 1-2
August 1985, pages 1-506
pp 1-13 August 1985
Physical principles determining the protein structure and protein folding are reviewed: (i) the molecular theory of protein secondary structure and the method of its prediction based on this theory; (ii) the existence of a limited set of thermodynamically favourable folding patterns of α- and β-regions in a compact globule which does not depend on the details of the amino acid sequence; (iii) the moderns approaches to the prediction of the folding patterns of α- and β-regions in concrete proteins; (iv) experimental approaches to the mechanism of protein folding. The review reflects theoretical and experimental works of the author and his collaborators as well as those of other groups.
pp 15-23 August 1985
The Chou-Fasman predictive algorithm for determining the secondary structure of proteins from the primary sequence is reviewed. Many examples of its use are presented which illustrate its wide applicability, such as predicting (a) regions with the potential for conformational change, (b) sequences which are capable of assuming several conformations in different environments, (c) effects of single amino acid mutations, (d) amino acid replacements in synthesis of peptides to bring about a change in conformation, (e) guide to the synthesis of polypeptides with definitive secondary structure,e.g. signal sequences, (f) conformational homologues from varying sequences and (g) the amino acid requirements for amphiphilicα-helical peptides.
pp 25-35 August 1985
Kuntz and Kauzmann have argued that dehydrating a protein results in conformational changes. In contrast, Rupleyet al. have developed a hydration model which involves no significant change in conformation; the onset of enzyme activity in hen egg-white lysozyme at hydration values of about 0.2 g water/g protein they ascribe rather to a solvation effect. Using a direct difference infra-red technique we can follow specific hydration events as water is added to a dry protein. Conformational studies of lysozyme using laser Raman spectroscopy indicate changes in conformation with hydration that are complete just before measurable activity is found. Parallel nuclear magnetic resonance measurements of exchangeability of the main chain amide hydrogens, as a function of hydration from near dryness, suggest a hydration-related increase in conformational flexibility which occurs before-and is probably necessary for-the Raman-detected conformational changes. Very recent inelastic neutron scattering measurements provides direct evidence of a flexibility change induced by hydration, which is apparently necessary before the enzyme can achieve adequate flexibility for it to begin to function.
pp 37-44 August 1985
Recent experiments in this laboratory on structural transformations caused by controlled dehydration of protein crystals have been reviewed. X-ray diffraction patterns of the following crystals have been examined under varying conditions of environmental humidity in the relative humidity range of 100-75%: a new crystal form of bovine pancreatic ribonuclease A grown from acetone solution in tris buffer (I), the well-known monoclinic form of the protein grown from aqueous ethanol (II), the same form grown from a solution of 2-methyl pentan-2,4-diol in phosphate buffer (III), tetragonal (IV), orthorhombic (V), monoclinic (VI) and triclinic (VII) hen egg white lysozyme, porcine 2 Zn insulin (VIII), porcine 4 Zn insulin (IX) and the crystals of concanavalin A(X). I, II, IV, V and VI undergo one or more transformations as evidenced by discontinuous changes in the unit cell dimensions, the diffraction pattern and the solvent content. Such water-mediated transformations do not appear to occur in the remaining crystals in the relative humidity range explored. The relative humidity at which the transformation occurs is reduced when 2-methyl pentan-2,4-diol is present in the mother liquor. The transformations are affected by the crystal structure but not by the amount of solvent in the crystals. The X-ray investigations reviewed here and other related investigations emphasize the probable importance of water-mediated transformations in exploring hydration of proteins and conformational transitions in them.
pp 45-55 August 1985
The water structure of rhombohedral 2 Zn insulin crystal which contains about 280 water molecules and 0.55-0.60 mol citrate molecules per dimer has been studied by X-ray crystallographic refinement with 1.1 A resolution data. Atomic parameters of 83 fully occupied and 258 partially occupied water molecules and 0.3 mol of citrate were obtained. Full matrix least-squares method with isotropic temperature factor was used for the refinement of partially occupied water molecules. The water molecules in this crystal exist in one of the three states: fully occupied water, partially occupied water and water continuum, and a schematic model of water structure in protein crystal was proposed. The flexibility of water molecules is described.
pp 57-66 August 1985
Previous studies from this laboratory have shown that the thermolysin fragment 121–316, comprising entirely the“all-α” COOH-terminal structural domain 158–316, as well as fragment 206–316 (fragment FII) are able to refold into a native-like, stable structure independently from the rest of the protein molecule. The present report describes conformational properties of fragments 228–316 and 255–316 obtained by chemical and enzymatic cleavage of fragment FII, respectively. These subfragments are able to acquire a stable conformation of native-like characteristics, as judged by quantitative analysis of secondary structure from far-ultra-violet circular dichroism spectra and immunochemical properties using rabbit anti-thermolysin antibodies. Melting curves of the secondary structure of the fragments show cooperativity with a temperature of half-denaturationTmof 65–66°C. The results of this study provide evidence that it is possible to isolate stable supersecondary structures (folding units) of globular proteins and correlate well with predictions of subdomains of the COOH-terminal structural domain 158–316 of thermolysin.
pp 67-87 August 1985
The primary structure of ovomucoid shows considerable sequence homology at three contiguous regions which form structural domains I, II and III. In order to see whether or not the three domains fold similarly and acquire similar overall native conformation/shape, two fragments A and C were obtained by controlled peptic digestion of ovomucoid. The two fragments were investigated for their chemical composition, molecular weight, anti-tryptic activity, hydrodynamic behaviour, optical properties and acid denaturation. Results on molecular weight, amino acid composition and inhibitory acitivity show that the fragments A and C correspond respectively to domain I-II and domain III. Optical data suggested more exposure of tyrosine residues in the fragments than in the intact molecule. Domain III exists in a compact and globular conformation under native conditions whereas domain I-II and ovomucoid appear to possess asymmetric conformation. Results on acid denaturation show that the process is thermodynamically reversible and that inter-domain separation probably precedes denaturation of domains during acidification of ovomucoid.
pp 89-106 August 1985
Gene 63 from bacteriophage T4 encodes a single polypeptide with two independent enzyme activities, RNA ligase and tail fibre attachment. The DNA sequence of gene 63 has been determined and the gene cloned in an expression plasmid (pDR540) that contains the inducibletac promoter.Escherichia coli cells containing the plasmid (KR54) produce about 5–10% of their soluble protein as RNA ligase. A convenient isolation procedure for the enzyme is described from KR54 cells and the isolated product is indistinguishable from that obtainable from T4-infectedEscherichia coli. The enzyme reacts reversibly with ATP in the presence of Mg2+ to give a covalent AMP-enzyme adduct. It is shown by FAB mass spectrometric analysis of chymotryptic fragments of the adenylylated enzyme that the AMP is bound covalently to lysine residue 99.
Methods ofin vitro mutagenesis are described for gene 63 cloned in a bacteriophage M13 vector. By deletion mutagenesis it was shown that the C-terminal 20 % of the protein is not crucial for the RLi activity but the TFA activity, as measured by a complementation assay, is reduced. A method is described for the introduction of point mutations in gene 63 by use of AMV reverse transcriptase for error-directed repair polymerisation in gapped DNA heteroduplexes. In addition, a synthetic oligonucleotide mismatched at the 3′ end was used as a primer for reverse transcriptase catalysed repair polymerisation to force a single base change in the codon for Lys-99 to give the codon for Asn. The mutant protein has no detectable RNA ligase activity but retains tail fibre attachment activity.
pp 107-119 August 1985
Replacement of Mg (II), the natural activator of brain hexokinase (EC 188.8.131.52) by paramagnetic Mn (II) without affecting the physiological properties of the enzyme, has rendered brain hexokinase accessible to investigations by magnetic resonance methods. Based on such studies, a site on the enzyme, where Mn (II) binds directly with high affinity has been identified and characterized in detail. Use ofβ,γ-bidentate Cr (III) ATP as an exchange-inert analogue for Mn (II) ATP has shown that Mn (II) binding directly to the enzyme has no catalytic role but another Mn (II) ion binding simultaneously and independently to the enzyme through the nucleotide bridge participates in enzyme function. However, using this direct binding Mn (II) ion and a covalently bound spin label as paramagnetic probes a beginning has been made in mapping the ligand binding sites of the enzyme. Ultra-violet difference spectroscopy has revealed the presence of at least two glucose 6-phosphate locations on the enzyme one of which presumably is the high affinity regulatory site modulated by substrate glucose. Elution behaviour of the enzyme on a phosphocellulose column suggests that glucose induces a specific phosphate site on the enzyme to which the phosphate bearing regulatory ligands of the enzyme may bind.
pp 121-139 August 1985
The interactions of theω-amino acid ligandsε-aminocaproic acid andp-benzylaminesulphonic acid with the isolated kringle 4 domain from human plasminogen have been investigated by1H-nuclear magnetic resonance spectroscopy at 300 and 600 MHz. Overall, the data indicate that binding either ligand does not cause the kringle to undergo significant conformational changes. When p-benzylaminesulphonic acid is in excess relative to the kringles, progressive exchange-broadening and high field chemical shifts are observed for the proton resonances of the ligand. The largest effect is seen at the amino end of the molecule, which indicates that the — NH3+ group of the ligand penetrates deeper into the binding site than does the — SO3-. Ligand-binding causes signals from the ring-current shifted Leu46 CH3δ.δ groups and from a number of aromatic side-chains to shift. Depending on the ligand, the latter include Tyr-II (Tyr50), Tyr-V (an immobile ring), His-II and His-III imidazole groups and the three Trp indole groups present in kringle 4. In particular,p-benzylaminesulphonic acid-binding induces large high field shifts on the Trp-II H6 triplet and the Trp-III (Trp72) H2 singlet. On the other hand,ε-aminocaproic acid bound to kringle 4 exhibits large chemical shifts of its CH2 proton resonances, which indicates that the lysine-binding site is rich in aromatic side chains.
Overhauser experiments centered on thep-benzylaminesulphonic acid H2,6 and H3,5 aromatic transitions as well as on the shifted Trp-II and Trp-III signals reveal efficient cross-relaxation between these two indole side chains and thep-benzylaminesulphonic acid ring. These experiments also show that the side chains from Phe64, Tyr-II (Tyr50), Tyr-IV, and His-II (His31) interact with the ligand. In combination with reported chemical modification experiments that show requirement of Asp57, Arg71 and Trp72 integrity for ligand-binding, our study underscores the relevance of the Cys51-Cys75 loop in defining the kringles’ lysine-binding site. Furthermore, the Cys22-Cys63 loop is folded so as to place His31, His33, Tyr41 and Leu46 in proximity to the binding site. The involvement of residues within the Cys51-Cys75 loop in ligand-binding suggests that Trp-II and Tyr-IV may correspond to Trp62 and Tyr74, respectively. As shown by Overhauser experiments, these two residues are in close contact with each other. From these studies and from the shielding and deshielding effects caused byp-benzylaminesulphonic acid, we suggest that the ligand is sandwiched between the indole rings of Trp-II and Trp-III, which form part of the hydrophobic binding site.
pp 141-149 August 1985
Circular dichroism spectra of proteins are extremely sensitive to secondary structure. Nevertheless, circular dichroism spectra should not be analyzed for protein secondary structure unless they are measured to at least 184 nm. Even if all the various types ofβ-turns are lumped together, there are at least 5 different types of secondary structure in a protein (α-helix, antiparallelβ-sheet, parallelβ-sheet,β-turn, and other structures not included in the first 4 categories). It is not possible to solve for these 5 parameters unless there are 5 equations. Singular value decomposition can be used to show that circular dichroism spectra of proteins measured to 200 nm contain only 2 pieces of information, while spectra measured to 190 nm contain about 4. Adding the constraint that the sum of secondary structures must equal 1 provides another piece of information, but even with this constraint, spectra measured to 190 nm simply do not analyze well for the 5 unknowns in secondary structure. Spectra measured to 184 nm do contain 5 pieces of information and we have used such spectra successfully to analyze a variety of proteins for their component secondary structures.
pp 151-165 August 1985
The salient features of the differential equation model to study protein dynamics are presented with results for 19 proteins.
pp 167-178 August 1985
Free energy simulations using the Metropolis Monte Carlo method and the coupling parameter approach with umbrella sampling are described for several problems of interest in structural biochemistry; the liquid water, the hydrophobic interaction of alkyl and phenyl groups in water and solvent effects on the conformational stability of the alanine dipeptide and the dimethyl phosphate anion in water. Proximity analysis of results is employed to identify stabilizing factors. Implications of result with respect to the structural chemistry of proteins and nucleic acids is considered.
pp 179-196 August 1985
Conformation and calcium binding properties of a series of gastrin-related peptides, in which the glutamic acid sequence at the N-terminal portion of the molecule has been elongated step by step, have been investigated using circular dichroism spectroscopy. A working hypothesis about the structure of these hormones in trifluoroethanol has been proposed. The structure comprises aβ-bend located at the level of the sequence Ala-Tyr-Gly-Trp. A correlation between chain elongation and increase of biological potency has been observed. All examined peptides strongly interact with calcium ions in trifluoroethanol. The variation of the circular dichroism spectra upon calcium addition provided some information about the groups involved in the coordination of the ions. Our results allow the hypothesis of the presence of one binding site, located at the C-terminal portion of the molecule in the gastrin octapeptide, and of an additional site at the N-terminus, in the longer fragments. The carboxyl function of Asp and Glu side-chains, at the two ends of the molecules, are probably involved in the interaction with the metal ions.
pp 197-208 August 1985
The technique of nuclear Overhauser effect difference spectroscopy allows the determination, from1H nuclear magnetic resonance spectra, of those protons in a structure which are near in space to a selected, irradiated proton. The experiment is extremely powerful in the determination of structure in solution, and is sufficiently precise often to give stereochemical detail. The method was used in determination of the structures of the antibiotics of the teicoplanin complex (members of the vancomycin group), and the principles are briefly illustrated. Additionally, nuclear magnetic resonance pulse sequences can be used to edit13C spectra (separate the spectrum into four spectra, containing C, CH, CH2, and CH3 carbons), and this technique also aided the structure elucidation of the teicoplanin complex. Finally, it is emphasised that nuclear Overhauser effect difference spectroscopy can be used to determine the molecular details of drug binding sites, and an example is given.
pp 209-221 August 1985
We report here two sets of results on proline-containing linear peptides, one of which brings out the role of theβ-turn conformation in the structure of nascent collagen while the other points to the functional importance of the β-turn in calcium-binding proteins. Based on the data on peptides containing the -Pro-Gly-sequence, we had proposed and experimentally verified that theβ-turn conformation in these peptides is a structural requirement for the enzymic hydroxylation of the proline residues in the nascent (unhydroxylated) procollagen molecule. Our recent data, presented here, on the conformation of peptides containing both the -Pro-Gly- and -Gly-Pro-sequences reveal that while theβ-turn in the substrate molecule is required at the catalytic site of prolyl hydroxylase, the polyproline-II structure is necessary for effective binding at the active site of the enzyme. Thus, peptides containing either theβ-turn or the polyproline-II structure alone are found to act only as inhibitors while those with the polyproline-II followed byβ-turn serve as substrates of the enzyme. In another study, we have synthesized the two linear peptides: Boc-Pro-D-Ala-Ala-NHCH3 and Boc-Pro-Gly-Ala-NHCH3 each of which adopts, in solution, a structure with two consecutiveβ-turns, as judged from circular dichroism, infrared and nuclear magnetic resonance data. Drastic spectral changes are seen in these peptides on binding to Ca2+. Both the peptides show a distinct specificity to Ca2+ over Mg2+, Na+ and Li+. A conformational change in the peptides occurs on Ca2+ binding which brings together the carbonyl groups to coordinate with the metal ion. These results imply a functional role for theβ-turn in Ca2+ — binding proteins.
pp 223-238 August 1985
In this paper we investigate the effect of main chain isosteric replacement of specific amino acid residues by α-hydroxy acids. As part of a long term program specifically protected heptaglutamates were prepared and their circular dichroism and nuclear magnetic resonance spectra in various solvents were examined. From these experiments conformational preferences were deduced. We have also prepared oligo-(γ-methyl-glutamates) replacing the amino acids at specific positions along the chain with S-lactic acid and have elucidated the effect of these main chain isosteric replacements on oligopeptide structure.
Analogues of collagen also have been prepared with glycolic acid replacing specific glycine residues. We synthesized the model hexamers Ac-Ala-Gly-Pro-Ala-Gly-Pro-NHMe, Ac-Ala-Glc-Pro-Ala-Gly-Pro-NHMe, and Ac-Ala-Gly-Pro-Ala-Glc-Pro-NHMe in order to study their structural characteristics under various conditions. Preliminary nuclear magnetic resonance and circular dichroism results are presented.
pp 239-251 August 1985
Cyclic peptides form an interesting class of compounds for study by conformational analysis, by virtue of their unique conformational features and biological properties. The small cyclic peptides having 3-6 peptide units in their ring, show a variety of conformational characteristics such as occurrence ofcis peptide units, flexibility of peptide dimension and variety in hydrogen bonding. The different possible conformations of cyclic tri- and hexa-peptides are given and certain specific conformational features are discussed for cyclic tetra and pentapeptides. For higher cyclic peptides, the hydrogen bonding requirement for stability of the backbone of the ring, is seen to be kept to a minimum. These various features and their significance are examined and discussed in the light of energy minimization studies and analysis of available experimental data.
pp 253-262 August 1985
Conformational energy computations of the monopeptides from three achiral α,α-dialkylated glycyl residues with acyclic side chains (namely α,α-dimethyl-; α,α-diethyl-; and α, α-di-n-propylglycines) are reported as a function of the relevant N-Cα-C′ bond angle. In parallel, experimental studies were performed in the solid state (infrared absorption and X-ray diffraction) and in solution (infrared absorption and proton magnetic resonance) on the corresponding protected homo-peptide series (the former series to the dodecamer, the other two series to the pentamers). The results obtained unequivocally indicate that the preference from a helical to a fully extended conformation increases as side-chain bulkiness increases. The longest homo-peptides from α,α-dimethylglycine form stable 310-helices. A picture of the mode of self-association of the helical structures has also been determined. The results of the theoretical analyses fit well with the experimentally observed conformational properties in the solid state and in chloroform solution.
pp 263-271 August 1985
The opioid pentapeptide leucine-enkephalinamide and eleven of its analogues have been synthesised by the solid phase technique employing mostly 9-fluoroenylmethyloxycarbonyl amino acid active esters in the presence of 1-hydroxybenzotriazole. Both the conventional chloromethylated copolystyrene-2% divinylbenzene resin as well asp-alkoxybenzyl alcohol resin were employed and it was observed that yields were uniformly better with the latter resin. The analogues were made by affecting single or multiple replacements of amino acids involving positions 1,2 and 5. Some of the analogues were found to be more potent than morphine in the guinea pig ileum assay.
pp 273-291 August 1985
The interaction of pore-forming agents, such as Sendai virus, influenza virus (at pH 5 3), activated complement,Staphylococcus aureus α-toxin, melittin and polylysine, with the surface membrane of cells has been studied. In each case the following changes are initiated: collapse of membrane potential, leakage of ions, and leakage of phosphorylated metabolites. The changes can be inihibited by extracellular Ca2+ at physiological concentration; Mg2+ is less effective, and Zn2+ is more effective, than Ca2+ Ca2+ appears to act at a stage subsequent to the binding of pore-forming agent to cells. It is concluded that divalent cations are able to protect cells against the damaging effects of certain viruses, toxins or the components of activated complement in a manner that is worthy of further investigation.
pp 293-306 August 1985
A total of 19 different crystal forms of complexes of valinomycin or its analogues with monovalent cations have been observed. The crystal structure determinations of valinomycin potassium tetrachloroaurate and valinomycin rubidium tetrachloroaurate are given here.Including this work complete structure determinations have now been published on 7 with 2 more soon to appear. Comparisons of these structural results suggest that the valinomycin complex opens at the D-valyl (lactyl) end and that contacts are possible between the complexed cation and other molecules. Such contacts may play an important part in membrane transport.
pp 307-314 August 1985
Energy profiles have been established for the transport of Na+, K+ and Cs+ through the gramicidin A channel. In Urry’s head-to-headβ3.36.3 left-handed helical dimer structure, using a refined methodology for the calculation of intra and intermolecular interactions. The computations show the important role, for the energy profile and the position of the possible binding site, of the flexible ethanolamine chain, whose significance was till now overlooked. The calculations indicate that the barriers at the entrance and at the center of the channel should be in the order Na+ XXX K+ XXX Cs+ but predict also that the energies of the binding sites should be the greatest for Na+ and, then, comparable for K+ and Cs+. The indications concerning the barriers are confirmed by experiment.
pp 315-327 August 1985
The electrostatic potential of valinomycin in various conformations as obtained by the crystal structures (uncomplexed, complexed) and theoretical considerations have been evaluated and compared. The potential energy profiles along the æ axis of the bracelet-like structures show a systematic variation from the uncomplexed to the complexed structure. This type of conformational change and the potential variation are probably associated with different states of ion transport, like the capture and release of ions by the ionophore. Also, the asymmetry of the molecule due to D-HyIV on one side and L-Lac on the other side is reflected in the potential values along the Z-axis, the magnitude of which, is considerable in the uncomplexed structure. The evaluation of the potential at the ab-initio level on smaller fragments indicate that the order of liganding capacity of oxygen is amide > ether > ester. Also, the inductive effects due to alkyl substitution is negligible as evidenced by the potential studies on the substituted amides and esters.
pp 329-342 August 1985
An earlier model in which uptake of essential nutrients for which the cell is auxotrophic, regulates cell division, is discussed in the light of new experimental findings, specifically the purification of a new type of transport-inhibitory protein from rat liver and the properties of the protein. The possible role of such proteins in malignant transformation is also discussed.
pp 343-354 August 1985
Several molecules like ionophores, vitamins, ion-binding cyclic peptides, acidic phospholipids, surfactants are known to expose the inner side of vesicles, to the externally added cations. Whereas ionophores and certain other systems bring about these changes by a selective transport (influx) of the cation by specialized mechanisms known as the carrier and channel mechanism, other systems cause lysis and vesicle fusion. These systems have been successfully studied using1H,31 P and13C nuclear magnetic resonance spectroscopy after the demonstration, fifteen years ago, of the ability of paramagnetic lanthanide ions to distinguish the inside of the vesicle from the outside. The results of these ’nuclear magnetic resonance kinetics’ experiments are reviewed.
pp 355-362 August 1985
Various structural components of biological membranes are asymmetrically localized in the two surfaces of the membrane bilayer. This asymmetry is absolute for membrane (glyco) proteins, but only a partial asymmetry has been observed for membrane phospholipids. In the red cell membrane, choline-phospholipids are localized mainly in the outer monolayer whereas aminophospholipids are distributed almost exclusively in the inner monolayer. Several evidences are now available to suggest that this distribution of membrane phospholipids in red cells is directly or indirectly maintained by the membrane-associated cytoskeleton (membrane skeleton). This belief is well supported by the previous as well as recent studies carried out in the authors laboratory. Previously, it has been shown that lipid-lipid interactions play no major role in maintaining the transmembrane phospholipid asymmetry in erythrocytes, and that the asymmetry is lost upon covalent crosslinking of the major membrane skeletal protein, spectrin. The recent data presented here further shows that degradation or denaturation of spectrin indices rapid transbilayer movement of membrane phospholipids in the cells which, in turn, leads to more random phospholipid distributions across the membrane. These studies taken together strongly suggest that the skeleton-membrane associations are the major determinants of the transmembrane phospholipid asymmetry in erythrocytes, and that the dissociation of the skeleton from the membrane bilayer probably results in generation of new reorientation sites for phospholipids in the membrane.
pp 363-374 August 1985
Surface-enhanced Raman spectra of membrane protein, located in native mem brane, bacteriorhodopsin, adsorbed by silver electrodes and hydrosols have been obtained for the first time. The distance between the retinal Schiff’s base and the external side of purple membrane of Halobacteriim halobiim was shown to be 6–9 A.
The possible distribition of the point charges aroind protonated retinal Schiff’s base has been proposed on the basis of the resonance Raman data and quantim chemical CNDO/S-CI calculations. Such a model contains tyrosine residue located near the retinal Schiff’s base and connected with COO- groipvia hydrogen bond COO- group acts as a protonated Schiff’s base counterion. The distance between oxygen atoms of COO- group and retinal Schiff’s base plane is 2.5–3.0A. The hydrogen bond (O-H. . .O-) length between oxygen atom of OH-group and oxygen atom of COO- group has been chosen 2.7±0.1Å Tyrosine hydroxyl group is located at 2.8–3.5 A from retinal Schiff’s base plane.
It was shown that in contrast to generally accepted Honig and Nakanishi model the spectral properties of Brh570, K610, L550 and M4Ï2 forms of bacteriorhodopsin photocycle as well as observed tyrosine deprotonation and COO- group protonation during M412 formation can be explained reasonably well by the suggested charge distribution. Furthermore, such a model of bacteriorhodopsin active site microenvironment allows to explain catalyzing of photo-induced protonated retinal Schiff’s base deprotonation observed in our preliminary experiments.
pp 375-387 August 1985
A review is presented focussing attention on the structural molecular biology of polysaccharides and complex carbohydrates, using examples obtained from terraqueous plants, animals, bacteria and insects The type and sequence of the condensation linkages in polysaccharides dominate their conformation, flexibility and interactions The extensive variety of geometries is overlaid by the constituent saccharide units themselves, decoration by side appendages and post-polymerisation chemical and structural modification X-ray diffraction information from oriented samples and computerised modelling has been used to analyse molecular conformation and geometry In general the relationship between glycosidic linkage geometry and conformation for the chemically simpler polysaccharides is understood In the case of more complex carbohydrates, unique solutions using diffraction methods alone are harder to establish In mixed protein carbohydrate systems, such as the glycoprotein antifreezes and protein-polysaccharide fibrous composites in insect cuticle, novel features in structure, morphology and interactions can usefully be explored and examined.
pp 389-401 August 1985
The possible modes of binding of kojibiose, nigerose, maltose and ManPα(1 → 2)Man to concanavalin A have been investigated using computer modelling studies. While α12 linked disaccharides bind to concanavalin A in two modes,i.e. by placing the reducing as well as non-reducing sugar units in the sugar binding site, nigerose or maltose can bind only in one mode,i.e. by placing the non-reducing sugar unit in the binding site. Though, both the sugar residues in α 12 linked disaccharides can reach the binding site, the preference is high for the non-reducing unit. When the non-reducing residue, in any of these disaccharides, enters the binding site, the allowed orientations and the possible hydrogen bonds with the protein seem to be independent of the glycosidic linkage. However, the number of hydrogen bonds the outward sugar residue forms with the protein are dependent on the type of linkage. Atleast one of the hydroxyl groups adjacent to the glycosidic linkage on the outward sugar residue is involved in the formation of a hydrogen bond with the protein suggesting the presence of an extended binding site. The orientation of the reducing sugar residue in the extended binding site is dependent on the linkage. Its orientation in nigerose is flipped when compared to that found in kojibiose or maltose leading to different non-covalent interactions with the protein which affect their binding affinities.
pp 403-411 August 1985
A chitooligosaccharide specific lectin (Luffa acutangula agglutinin) has been purified from the exudate of ridge gourd fruits by affinity chromatography on soybean agglutinin-glycopeptides coupled to Sepharose-6B. The affinity purified lectin was found homogeneous by polyacrylamide gel electrophoresis, in sodium dodecyl sulphate-polyacrylamide gels, by gel filtration on Sephadex G-100 and by sedimentation velocity experiments. The relative molecular weight of this lectin is determined to be 48,000 ±1,000 by gel chromatography and sedimentation equilibrium experiments. The sedimentation coefficient (S20, w) was obtained to be 4.06 S. The Stokes’ radius of the protein was found to be 2.9 nm by gel filtration. In sodium dodecyl sulphate-polyacrylamide gel electrophoresis the lectin gave a molecular weight of 24,000 in the presence as well as absence of 2-mercaptoethanol. The subunits in this dimeric lectin are therefore held by non-covalent interactions alone. The lectin is not a glycoprotein and circular dichroism spectral studies indicate that this lectin has 31% α-helix and no β-sheet. The lectin is found to bind specifically to chitooligosaccharides and the affinity of the lectin increases with increasing oligosaccharide chain length as monitored by near ultra-violet-circular dichroism and intrinsic fluorescence titration. The values of ΔG, ΔH and ΔS for the binding process showed a pronounced dependence on the size of the oligosaccharide. The values for both ΔH and ΔS show a significant increase with increase in the oligosaccharide chain length showing that the binding of higher oligomers is progressively more favoured thermodynamically than chitobiose itself. The thermodynamic data is consistent with an extended binding site in the lectin which accommodates a tetrasaccharide. Based on the thermodynamic data, blue shifts and fluorescence enhancement, spatial orientation of chitooligosaccharides in the combining site of the lectin is assigned.
pp 413-424 August 1985
Two fucsyltransferases (FucT-2 and FucT-3) have been solubilized from Golgi-rich membrane fraction of bovine spleen, using a cationic detergent. FucT-3 was distinguished from FucT-2 by comparing their kinetic parameters and heat stability. FucT-2 and FucT-3 lost activity (85 %) and (5 %), respectively, when heated at 55°C for 10 sec. Two galactosyltransferases (GalT-3 and GalT-4) and two sialyltransferases (SAT-2 and SAT-3) have also been solubilized from embryonic chicken brain membranes using nonionic detergents. Affinity chromatography and microisoelectric focusing were used to separate these enzymes into functionally pure fractions. Anomeric and positional linkages in some of the products (LM1 and LD1c) have also been established. The terminal NeuAc(α2-8) linkage in GD3 and LD1c was established by identification of the partially methylated penultimate [Ac-14C]sialic acid.
pp 425-436 August 1985
This contribution illustrates the advantages of some chromophoric and fluorophoric carbohydrate derivatives such asp-nitrophenyl (pNO2Phe) or 4-methylumbelliferyl (MeUmb) glycosides andN-dansylgalactosamine in studies of the binding equilibrium and kinetics with some plant lectins. The methods used involve continuous titrations of changes in ligand or protein absorption and ligand fluorescence, including substitution titrations as well as stopped-flow, temperature-jump or pressure-jump relaxation kinetics.
When monitored by temperature-jump relaxation, binding of MeUmbαGal to the bloodgroup A specific lectin GSAI-A4 fromGriffonia simplicifolia is a simple bimolecular association with parametersk+= 9.4 × 104 M-1 s-1 andk-1 = 5.3 s-1 at 23°C, but binding to the GSAI-B4 lectin is biphasic.
The complementarity of the peanut agglutinin binding site with Galβ1 → 3GalNAc that occurs in manyO-glycoproteins follows from enthalpic considerations and also from the value of the dissociation-rate parameterk-1 = 0.24 s-1 of the MeUmbβGalβl → 3GalNAc.lectin complex. This value, obtained by stopped-flow kinetics is 100 times smaller than for other mono-and disaccharides investigated. The binding mechanism is simple and the derivatisation of Galβ1 → 3GalNAc does not affect the affinity to a considerable degree.
The binding preference of tetravalentsoybean agglutinin for MeαGalNAc over MeαGal by a factor of 25 is mainly of enthalpic origin with an additional 7 kJ mol-1; the NAc group causes perturbation of a tryptophanyl residue, evidenced by protein difference absorption spectrometry. In the glycosides, a large aglycon likeβpNO2 Phe orβMeUmb hardly affects the affinity of SBA but a largeN-dansyl group increases the affinity by a factor 20 as compared to GalNAc. The 10-fold increase in carbohydrate-specificN-dansylgalactosamine fluorescence, together with a very favourable entropic contribution point at the presence of a hydrophobic region in the vicinity of the carbohydrate-binding site. The dissociation-rate parameter of the MeUmbβGalNAc SBA complex is slower than for any reported monosaccharide-lectin complex: 0.4 s-1.
The divalent lectin fromErythrina cristagalli preferentially binds the Galβ1 → 4GlcNAc structure that occurs in manyN-glycoproteins. The combining site was mapped thermodynamically with carbohydrates ranging from mono-to pentasaccharides as derived fromN-glycoproteins. Here, N-dansylgalactosamine was used as a fluorescent indicator ligand in substitution titrations. When Galβ1 → 4GlcNAc was linkedα1 → 2 orα1 → 6 to Man, the binding enthalpy and entropy remained practically constant. Application of stopped flow kinetics and pressure-jump relaxation withN-dansylgalactosamine gave mono-exponential signal changes with a concentration dependence corresponding tok+ = 4.8 x 104 M-1 s-1k- = 0.4 to 0.66 s-1 and a change in reaction volume of+7ml/mol.
pp 437-450 August 1985
In crystalline cyclodextrin hydrates O-H . . . O hydrogen bonds occur in homo-dromic chainlike and cyclic motifs. Inβ-cyclodextrin. 11 H2O, where OH-groups are disordered, flip-flop hydrogen bonds O-(1/2H) . . . (1/2H)-O are found which represent a dynamical equilibrium O-H . . . 0⇌0 . . . H-O. Detailed insight into otherwise hidden structural aspects of hydration and water structure (clusters) become available.
pp 451-460 August 1985
Troponin C is the Ca2+-binding subunit of the troponin complex and is involved in the calcium control of muscle contraction. The X-ray structure of chicken TnC has been determined at 3Å resolution using a single heavy atom derivative and application of a novel phase improvement and phase extension procedure. The protein has an unusual dumbbell-shape with a length of about 70A. The N- and C-domains are connected by a single long α-helix of about 9 turns. Two metal binding sites (the Ca2+-Mg2+ sites) in the C-domain are occupied by metal ions in the crystals and the helix-loop-helix Ca2+ -binding folds are very similar to those in other known Ca2+ -binding proteins. In contrast, the Ca2+ -specific sites in the N-domain appear unoccupied and the two putative Ca2+ -binding folds have a vastly different structural arrangement. The conformational rearrangements in the N-domain upon Ca2+ binding are believed to be the trigger for a cascade of protein-protein interaction alterations which lead to muscle contraction.
pp 461-470 August 1985
Binding proteins, which are located in the periplasmic space of Gram-negative bacteria, are essential components of osmotic shock-sensitive active transport systems and Chemotaxis. Described briefly herein are the high resolution molecular structures of four binding proteins specific for (i) L-arabinose, (ii) sulphate, (iii) D-galactose, and (iv) leucine, isoleucine or valine which we have recently determined. The first three proteins contained bound substrates. Several novel substrate binding properties of the arabinose- and sulphate-binding proteins as revealed by structure refinement at 1.7 Å resolution are also presented. These results have profound significance in understanding both protein structures and substrate-protein interactions.
pp 471-479 August 1985
The three-dimensional structure of the heme-containing fungal catalase fromPenicillium vitale (m.m. 2,80,000) has been studied by X-ray analysis at 2.0 A resolution. The molecule is tetramer, each subunit contains 670 aminoacid residues identified to construct “X-ray” primary structure. The subunit is built of three compact domains and their connections. The first domain of about 350 residues contains aβ-barrel flanked by helices, the second domain of 70 residues is formed by four helices and the third one is composed of 150 residues and is topologically similar to flavodoxin. The active site including heme is deeply buried near theβ-barrel.
A comparison of the structure of catalase fromPenicillium vitale with that of beef liver catalase revealed very close structural homology of the first and the second domain, but the third domain is entirely absent in beef liver catalase.
A catalase from thermophillic bacteriaThermus thermophilus (m.m. 2,10,000) has been first isolated, crystallized and studied by X-ray analysis. Crystals are cubic, space group is P213, a = 133.4 Å. The molecule is a hexamer with trigonal symmetry 32. The electron density map at 3 Å resolution made it possible to trace the polypeptide chain. The main structural motif is formed by four near parallel helices. There is no heme inThermus thermophilus catalase, the active site is between the four helices and contains two manganese ions.
pp 481-489 August 1985
Crystal structure of subtilisin complexed with its trapped substrateStreptomyces subtilisin inhibitor—Protein-protein interaction and evolution of serine proteinases and their proteinaceous inhibitors
The complex of a bacterial alkaline serine proteinase, subtilisin BPN’, with its proteinaceous inhibitorStreptomyces subtilisin inhibitor is unique in several respects, compared with other similar complexes containing serine proteinases of trypsin family. In addition to the usual antiparallelβ-sheet involving P1-P3 residues of the inhibitor, P4-P6 residues form antiparallelβ-sheet with a previously unnoticed chain segment (the ‘S4-6 site’) of subtilisin. The ‘S4-6 site’ does not exist in serine proteinases of trypsin family, whether of mammalian or microbial origin. Global induced-fit movement seems to occur on the ‘trapped substrate’Streptomyces subtilisin inhibitor: a channel-like structure in SSI remote from the contact region becomes about 2 Å wider upon complexing with subtilisin. Main role of the secondary contact region ofStreptomyces subtilisin inhibitor seems to support the reactive site loop (primary contact region). Steric homology for the two contact regions is so high between the inhibitors ofStreptomyces subtilisin inhibitor family and those of pancreatic secretory trypsin inhibitor-ovomucoid inhibitor family that it seems to favour a divergent evolution and to support the general notion as to the relationship of prokaryotic and eukaryotic genes put forwarded by Doolittle(Nature (London),272, 581, 1978).
pp 491-498 August 1985
The molecular mechanism of drug action has been studied by X-ray diffraction analysis of human carbonic anhydrase I complexed with two different sulphonamides. The acetazolamide and amino benzene sulphonamide are found to bind to the catalytically essential zinc ion thereby inhibiting the function of the enzyme. The inhibitor molecules are stabilized in the active site of the protein by van der Waals interaction with a number of protein side chain groups.
pp 499-506 August 1985
The X-ray structure determination of yeast phosphoglycerate kinase and subsequent substrate binding studies have helped to define the binding sites for the triose and nucleoside phosphate substrates. This communication deals with one feature of the binding site—the location of an aspartic acid residue close to the phosphoryl binding site of the nucleotide substrate—and relates this and other structural features of the active site to the properties of this enzyme as deduced from nuclear magnetic resonance studies.
Volume 44 | Issue 5
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