Hydrogen-tritium exchange kinetics of soybean trypsin inhibitor (Kunitz). Solvent accessibility in the folded conformation.

The hydrogen exchange kinetics of Kunitz soybean trypsin inhibitor (STI) has been studied at pH 2, 3, and 6.5. From the temperature dependence of proton exchange at low pH, THE CONTRIBUTION OF MAJOR, REVERSIBLE PROTEIN UNFOLDING To the hydrogen exchange kinetics has been determined. Exchange directly from the folded conformation is characterized by an apparent activation energy (E*app) of approximately 25 kcal/mol, close to that of the chemical exchange step. At pH 6.5 the protein is more temperature stable than at low pH, and exchange of all but congruent to 8 protons can be observed to exchange with E*app congruent to 27 kcal/mol. This implies that all but congruent to 8 protons are accessible to exchange with solvent in the solution structure of folded STI. Estimates can be made of the average number of water molecules per molecule of STI consistent with a solvent accessibility model of hydrogen exchange kinetics. These estimates indicate that very few water molecules within the protein matrix are necessary to explain the exchange data. Calculations are done for the STI hydrogen exchange kinetics at pH 3, 30 degrees, approximating STI structure by a sphere of radius = 18 A. These calculations indicate an average of congruent to 4 water molecules in the shell from 13 to 16 A. from the center of the molecule, while less than 1 water molecule is indicated in the innermost 13 A. These calculations also suggest that there are congruent to 190 water molecules associated with the outermost 1.5-2 A of the sphere. While these values are consistent with a hydrophobic region in the central protein matrix, they indicate more solvent accessibility in the outer 1/3 of the molecule than the static accessibility estimates made from X-ray coordinates. Our results suggest that any protein movements or fluctuations responsible for solvent accessibility in proton exchange processes are localized in the outer regions of the globular structure.     

Conformational states of pancreatic lipase

Spin-label method was applied to the studies of conformation properties of pancreatic lipase. Spin-labelled derivatives of the enzyme in SH- and NH2-groups were obtained. ESR-spectra of both samples belong to the immobilized type, in the first case the ESR-spectrum corresponding to strong immobilization of the spin-label, and in the second--to the average one. In both cases the rotation correlation time of the enzyme molecule was measured. The time proved the same independent of the site of the label attachment; it corresponded to the rotation of macromolecule with molecular weight 50000. This fact points to the absence of both intramolecular flexibility of the enzyme molecule and of the association of lipase molecules in solution. It has been shown that introduction of substrates and inhibitors of the enzyme and the interface as well, induces no changes in the ESR spectra, which points to the absence of local conformation changes of protein near the spin-labels introduced.     

Direct evidence for the alterations in protein structure and conformation upon in vitro nonenzymatic glycosylation.

The formation of nonenzymatic glycosylation products appears to be a link between chronic hyperglycaemia and long-term diabetic complications. However, little is known concerning the glycation-induced modifications in the structure and conformation of proteins, which possibly underlie their altered functional characteristics. This study conveys a direct evidence for and compares the glucose-induced modifications in the conformation of three proteins with various half-lives: bovine serum albumin, human haemoglobin and bovine tendon collagen. These proteins incubated in vitro with glucose in various media containing optionally EDTA and Fe2+ ions contained up to 4-10 times as much attached glucose as did their relevant controls, and the extent of glycation was the highest in the samples incubated under air or in the absence of EDTA. The fluorescence and ESR data indicate that the Trp in albumin molecule, given albumin glycation-induced structural modifications, became more exposed to water surrounding solution whereas the Trp residues of haemoglobin remained shielded from water; also collagen fluorescence derived from the supposedly newly formed covalent crosslinks is vastly increased, and particularly when collagen was glycated under air or in the presence of Fe2+ ions. Possible mechanisms underlying the increased mobility of selected protein domains and glycation-mediated alterations in protein conformation are considered and discussed.     

Mass-weighted molecular dynamics simulation and conformational analysis of polypeptide.

Atomic motions in protein molecules have been studied by molecular dynamics (MD) simulations; dynamics simulation methods have also been employed in conformational studies of polypeptide molecules. It was found that when atomic masses are weighted, the molecular dynamics method can significantly increase the sampling of dihedral conformation space in such studies, compared to a conventional MD simulation of the same total simulation time length. Herein the theoretical study of molecular conformation sampling by the molecular dynamics-based simulation method in which atomic masses are weighted is reported in detail; moreover, a numerical scheme for analyzing the extensive conformational sampling in the simulation of a tetrapeptide amide molecule is presented. From numerical analyses of the mass-weighted molecular dynamics trajectories of backbone dihedral angles, low-resolution structures covering the entire backbone dihedral conformation space of the molecule were determined, and the distribution of rotationally stable conformations in this space were analyzed quantitatively. The theoretical analyses based on the computer simulation and numerical analytical methods suggest that distinctive regimes in the conformational space of the peptide molecule can be identified.     

Structural studies by proton magnetic relaxation of stereochemical probes. II. Allosteric effects in human methaemoglobin.

The haem-iron accessibility to solvent molecules in human aquomet- and fluoromethaemoglobin was studied by the magnetic relaxation of protons from a stereochemical probe (methanol in deuterated solutions) in its dependence on allosteric effects induced by inositol hexaphosphate and pH between 5.5 and 8.5. The exchange of methanol with bulk solvent was observed only when inositol hexaphosphate was bound to aquomethaemoglobin, which is consistent with a widening of the haemcrevice compared to the conformation in the absence of inositol hexaphosphate. An increase in alkalinity in the physiological range of the Bohr effect results in a gradual impedence of the solvent dynamics inside the haem-pocket. The fast-relaxation phase of methyl protons indicates that a large number of methanol molecules are under the strong influence of the protein; this effect is considerably smaller with inositol hexaphosphate bound to aquomethaemoglobin. The hypothesis which implies a proton from the coordinated water molecule is responsible for the observed relaxation rates has been critically discussed. The model with a water molecule exchanging between a position next to the sixth-ligand site of the haem-iron and the bulk solvent is further substantiated experimentally. This model has been found to be the simplest and most self consistent in the interpretation of all these proton magnetic relaxation data.     

Synthesis and characterization of stacked and quenched uridine nucleotide fluorophores.

Intramolecular aromatic interactions in aqueous solution often lead to stacked conformation for model organic molecules. This designing principle was used to develop stacked and folded uridine nucleotide analogs that showed highly quenched fluoroscence in aqueous solution by attaching the fluorophore 1-aminonaphthalene-5-sulfonate (AmNS) to the terminal phosphate via a phosphoramidate bond. Severalfold enhancement of fluorescence could be observed by destacking the molecules in organic solvents, such as isopropanol and dimethylsulfoxide or by enzymatic cleavage of the pyrophosphate bond. Stacking and destacking were confirmed by 1-H NMR spectroscopy. The extent of quenching of the uridine derivatives correlated very well with the extent of stacking. Taking 5-H as the monitor, temperature-variable NMR studies demonstrated the presence of a rapid interconversionary equilibrium between the stacked and open forms for uridine-5'-diphosphoro-beta-1-(5-sulfonic acid) naphthylamidate (UDPAmNS) in aqueous solution. DeltaH was calculated to be -2.3 Kcal/mol, with 43-50% of the population in stacked conformation. Fluorescence lifetime for UDPAmNS in water was determined to be 2.5 ns as against 11 ns in dimethyl sulfoxide or 15 ns for the pyrophosphate adduct of AmNS in water. Such a greatly reduced lifetime for UDPAmNS in water suggests collisional interaction between the pyrimidine and thefluorophore moieties to be responsible for quenching. The potential usefulness of such stacked and quenched nucleotide fluorophores as probes for protein-ligand interaction studies has been briefly discussed.     

Solvent accessibilities in glycyl, alanyl and seryl dipeptides.

Theoretical studies on glycyl-alanyl and seryl dipeptides were performed to determine the probable backbone and side-group conformations that are preferred for solvent interaction. By following the method of Lee & Richards [(1971) J. Mol. Biol. 55, 379-400], a solute molecule is represented by a set of interlocking spheres of appropriate van der Waals radii assigned to each atom, and a solvent (water) molecule is rolled along the envelope of the van der Waals surface, and the surface accessible to the solvent molecule, and hence the solvent accessibility for a particular conformation of the solute molecule, is computed. From the calculated solvent accessibilities for various conformations, solvation maps for dipeptides were constructed. These solvation maps suggest that the backbone polar atoms could interact with solvent molecules selectively, depending on the backbone conformation. A conformation in the right-handed bridge (zetaR) region is favoured for both solvent interaction and intrachain hydrogen-bonding. Also the backbone side-chain hydrogen-bonding within the same dipeptide fragment in proteins is less favoured than hydrogen-bonding between side chain and water and between side chain and atoms of other residues. Solvent accessibilities suggest that very short distorted alphaR-helical and extended-structural parts may be stabilized via solvent interaction, and this could easily be possible at the surface of the protein molecules, in agreement with protein-crystal data.     

Cell Adhesion Molecule L1 in Folded (Horseshoe) and Extended Conformations

We have investigated the structure of the cell adhesion molecule L1 by electron microscopy. We were particularly interested in the conformation of the four N-terminal immunoglobulin domains, because x-ray diffraction showed that these domains are bent into a horseshoe shape in the related molecules hemolin and axonin-1. Surprisingly, rotary-shadowed specimens showed the molecules to be elongated, with no indication of the horseshoe shape. However, sedimentation data suggested that these domains of L1 were folded into a compact shape in solution; therefore, this prompted us to look at the molecules by an alternative technique, negative stain. The negative stain images showed a compact shape consistent with the expected horseshoe conformation. We speculate that in rotary shadowing the contact with the mica caused a distortion of the protein, weakening the bonds forming the horseshoe and permitting the molecule to extend. We have thus confirmed that the L1 molecule is primarily in the horseshoe conformation in solution, and we have visualized for the first time its opening into an extended conformation. Our study resolves conflicting interpretations from previous electron microscopy studies of L1.     

Bovine serum albumin in lithium chloride solutions.

The effects of li+ and H3O+ on the conformation of bovine serum albumin in azqueous solutions at room temperature are compared. At low pH (high concentration of H3O+) the change in conformation of the protein is demonstrated by an increase in effective volume, a decrease in helical content and a blue shift of tyrosyl residue. A similar change is observed for the protein in highly concentrated LiC1 solution (6.0-7.0M) at neutral pH. However, the H3O+ is 12,000 times more powerful than the Li+ in destabilizing the protein molecule. This is consistent with their thermodynamic and kinetic properties, since the H3O+ is often different from the Li+ in several orders of magnitude. While the changes in structural properties of the protein are almost identical in both the acidic solution and the highly concentrated LiC1 solution, further study using dioxane as a probe suggests different mechanisms under which the changes occur. The effect of H3O+ is related to electrostatic force, whereas the effect of Li+ is related to both the electrostatic hydrophobic forces. These two major forces are believed to be responsible for the conformation of protein molecules.     

Conformational stability of antamanide and analogs. Crystal structure of perhydrosymmetric antamanide, cyclic (-Val-Pro-Pro-Cha-Cha-Val-Pro-Pro-Cha-Cha-)

The synthetic perhydrogenated symmetric analog of the cyclic decapeptide antamanide is biologically inactive, although the conformation of the molecule and the crystal packing are very similar to that of the active symmetric analog of antamanide. In fact, the same conformation for the molecule has now been found in six polymorphs of uncomplexed antamanide and its analogs. The differences between the active and inactive antamanide analogs are displayed dramatically in the conformations of their metal ion (Na+ or Li+) complexes, thus suggesting strongly that for physiological activity antamanide is not in the conformation assumed by the uncomplexed molecule, but rather in the conformation assumed by the complexed state of natural antamanide. The present structure crystallizes in space group P2(1)2(1)2(1) with a = 20.515(14) A, b = 21.316(16) A, c = 17.128(16) A and four peptide molecules in the unit cell. There are three cocrystallized water molecules at full occupancy intrinsic to the peptide, and several more water molecules or other solvent molecules at partial occupancy. The formula of the peptide is C66H106N10O10.4-H2O.2X.     

Enhancement of catalytic efficiency of enzymes through exposure to anhydrous organic solvent at 70 degrees C. Three-dimensional structure of a treated serine proteinase at 2.2 A resolution

The enzyme behavior in anhydrous media has important applications in biotechnology. So far chemical modifications and protein engineering have been used to alter the catalytic power of the enzymes. For the first time, it is demonstrated that an exposure of enzyme to anhydrous organic solvents at optimized high temperature enhances its catalytic power through local changes at the binding region. Six enzymes: proteinase K, wheat germ acid phosphatase, alpha-amylase, beta-glucosidase, chymotrypsin and trypsin have been exposed to acetonitrile at 70 degrees C for three hours. The activities of these enzymes were found to be considerably enhanced. In order to understand the basis of this change in the activity of these enzymes, the structure of one of these treated enzymes, proteinase K has been analyzed in detail using X-ray diffraction method. The overall structure of the enzyme is similar to the native structure in aqueous environment. The hydrogen bonding system of the catalytic triad is intact after the treatment. However, the water structure in the substrate binding site undergoes some rearrangement as some of the water molecules are either displaced or completely absent. The most striking observation concerning the water structure pertains to the complete deletion of the water molecule which occupied the position at the so-called oxyanion hole in the active site of the native enzyme. Three acetonitrile molecules were found in the present structure. All the acetonitrile molecules are located in the recognition site. The sites occupied by acetonitrile molecules are independent of water molecules. The acetonitrile molecules are involved in extensive interactions with the protein atoms. All of them are interlinked through water molecules. The methyl group of one of the acetonitrile molecules (CCN1) interacts simultaneously with the hydrophobic side chains of Leu-96, Ile-107, and Leu-133. The development of such a hydrophobic environment at the recognition site introduces a striking conformation change in Ile-107 by rotating its side chain about C(alpha)--C(beta) bond by 180 degrees to bring about the delta-methyl group within the range of attractive van der Waals interactions with the methyl group of CCN1. A similar change has earlier been observed in proteinase K when it is complexed to a substrate analog lactoferrin fragment.     

Structure of macrocyclic K+, Rb+-complexon of meso-valinomycin monohydrate, cyclo[-(D-Val-Hyi-Val-D-Hyi)3-].H2O, in a crystalline complex with dioxane by x-ray structural data]

The crystal structure of a valinomycin analogue, cyclo[-(D-Val-Hyi-Val-D-Hyi)3-]x(C60H102N6O18) crystallized with dioxane and water molecules, has been solved by X-ray direct methods. The conformation found is analogous to one established for free meso-valinomycin crystallized from other organic solvents. It is characterized by a centrosymmetric bracelet form, stabilized by six intramolecular 4----1 type hydrogen bonds between amide N-H and C = O groups. One water molecule is fixed asymmetrically by hydrogen bonds in the internal negatively charged cavity of the complexon. The meso-valinomycin molecule "bracelets" in the crystal form stacks alternatively with dioxane molecules.     

Molecular structure of L-lysyl-L-tyrosyl-L-serine acetate

The structure of the tripeptide L-lysyl-L-tyrosyl-L-serine acetate was determined by X-ray diffraction. The crystals are triclinic space group P1, with two peptide molecules in the unit cell. The peptides are in zwitterionic form with positive charges both in the amino terminal and epsilon-amino groups of lysine. A negative charge is found in one of the carboxylic groups, whereas the other one is protonated. Both peptides show very similar backbone torsional angles, in the beta pleated sheet region, but different tyrosine and serine side-chain conformations. The two lysine side chains have a similar conformation g + tg + t, which had not been previously found. In the unit cell we also find one water molecule, one isopropanol molecule and four acetic acid molecules, three of them likely to be present as acetate anions. These molecules form layers which separate the beta-pleated sheets. The whole structure looks like an ordered solution of peptides in the beta-sheet conformation. An extensive network of hydrogen bonds stabilizes the crystal structure.     

Crystal structure of the complex of concanavalin A and tripeptide

The X-ray structure analysis of a cross-linked crystal of concanavalin A soaked with the tripeptide molecule as the probe molecule showed electron density corresponding to full occupation in the binding pocket. The site lies on the surface of concanavalin A and is surrounded by three symmetry-related molecules. The crystal structure of the tripeptide complex was refined at 2.4-Å resolution to an R-factor of 17.5%, (R_free factor of 23.7%), with an RMS deviation in bond distances of 0.01 Å. The model includes all 237 residue of concanavalin A, 1 manganese ion, 1 calcium ion, 161 water molecules, 1 glutaraldehyde molecule, and 1 tripeptide molecule. This X-ray structure analysis also provides an approach to mapping the binding surface of crystalline protein with a probe molecule that is dissolved in a mixture of organic solvent with water or in neat organic solvent but is hardly dissolved in aqueous solution.     

Solution conformation of lactate dehydrogenase as studied by saturation transfer ESR spectroscopy.

Several binary and ternary inhibitor and 'dead end' complexes of pig heart lactate dehydrogenase (L-lactate:NAD+ oxidoreductase, EC 1.1.1.27) were studied by saturation transfer ESR spectroscopy by means of an active NAD analog, spin-labeled at N6. The mobility of the spin-label depends on the nature of small molecules bound at the remote catalytic end of the coenzyme. The spin-label was found to serve as a reporter group monitoring the conformation of the peptide loop that is folded down over the active cleft in crystals of ternary complexes. The data suggest a fluctuation of the loop between open and closed forms in solution. The structure of the inhibitor molecules has been correlated with their ability to stabilize a more closed conformation of the loop.     

The conformation and aggregation of bovine β-casein A. I. Molecular aspects of thermal aggregation

The conformation of β-casein A in the monomeric and thermally aggregated states has been investigated by a range of techniques. β-Casein exists as a monomer in solution at 4°C and at concentrations up to at least 3 g/dl. The molecule is flexible and exhibits a lot of segmental motion, but its secondary structure is not wholly random coil; about one-third of the polypeptide chain is ordered and the likely locations of these regions are discussed. The radius of gyration, representing the time-average distribution of the flexible chain, is 46 Å. Increasing temperature leads to aggregation of the β-casein molecules. The degree of association is very sensitive to experimental conditions, and under our conditions a 14-mer exists at 20°C. The aggregate is spherical with a radius of about 100 Å. The interior of the aggregate is relatively disordered, and the β-casein molecules remain in a largely flexible, hydrated conformation. The volume restriction of the protein molecules which occurs on association leads to some immobilization of the hydrophobic C-terminal region, which is packed toward the center of the aggregate.     

On the dependence of molecular conformation on the type of solvent environment: a molecular dynamics study of cyclosporin A

The dependence of the conformation of cyclosporin A (CPA), a cyclic undecapeptide with potent immunosuppressive activity, on the type of solvent environment is examined using the computer simulation method of molecular dynamics (MD). Conformational and dynamic properties of CPA in aqueous solution are obtained from MD simulations of a CPA molecule dissolved in a box with water molecules. Corresponding properties of CPA in apolar solution are obtained from MD simulations of CPA in a box with carbontetrachloride. The results of these simulations in H2O and in CCl4 are compared to each other and to those of previous simulations of crystalline CPA and of an isolated CPA molecule. The conformation of the backbone of the cyclic polypeptide is basically independent of the type of solvent. In aqueous solution the beta-pleated sheet is slightly weaker and the gamma-turn is a bit less pronounced than in apolar solution. Side chains may adopt different conformations in different solvents. In apolar solution the hydrophobic side chain of the MeBmt residue is in an extended conformation with its hydroxyl group hydrogen bonded to the backbone carbonyl group. In aqueous solution this hydrophobic side chain folds over the core of the molecule and the mentioned hydrogen bond is broken in favor of hydrogen bonding to water molecules. The conformation obtained from the MD simulation in CCl4 nicely agrees with experimental atom-atom distance data as obtained from nmr experiments in chloroform. In aqueous solution the relaxation of atomic motion tends to be slower than in apolar solution.     

Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions.

A lattice model of proteins is introduced. "A protein molecule" is a chain of nown-intersecting units of a given length on the two-dimensional square lattice. The copolymeric character of protein molecules is incorporated into the model in the form of specificities of inter-unit interactions. This model proved most effective for studying the statistical mechanical characteristics of protein folding, unfolding and fluctuations. The specificities of inter-unit interactions are shown to be the primary factors responsible for the all-or-none type transition from native to denatured states of globular proteins. The model has been studied by the Monte Carlo method of Metropolis et al., which is now shown applied to approximately simulating a kinetic process. In the strong limit of the specificity of the inter-unit interaction the native conformation was reached in this method by starting from an extended conformation. The possible generalization and application of this method for finding the native conformation of proteins form their amino sequence are discussed.     

Thermodynamics of proteins in unusual environments

Some aspects of protein thermodynamics in unconventional environments are addressed and discussed. Aqueous medium, especially dilute solution is the 'usual' ambient, which mediates all the interactions between protein and nearby molecules. When the water content is low, the surroundings may be considered 'unusual', exerting new stresses on the protein molecule and demanding different responses and property changes. The unusual systems considered in this article are low-water protein environments, including nearly dry state powders, organic solvent dispersions and reverse micelles' inclusions. The changes of hydration experienced by the protein after immobilization on solid supports are emphasized with respect to the free bulk solution state. Finally, the aqueous medium altered by water connectivity perturbing agents (polysaccharides) or in macromolecular crowding conditions (in the presence of polyols) is also considered as highly not ideal protein environments. The different responses elicited by the protein under the stress induced by drastic surrounding alterations may give insights for the controlled exploitation of the protein's biological and thermodynamic properties.     

Conformational studies of corticotropin1-32 and constitutive peptides by circular dichroism.

Circular dichroism spectra on corticotropin1-32 and its constitutive N-, and C-terminal peptides are determined in water and trifluoroethanol under several conditions in the aromatic and peptide spectral regions. Furthermore, the effects of pH and varied mixtures of water-trifluoroethanol are examined on the corticotropin1-32 molecule. The results show that the N- and C-terminal series have a different behaviour in both aqueous and organic media. Corticotropin and the former peptides display "random" spectra in water, and alpha-helix type spectra in trifluoroethanol, while the latter have "random" spectra in both solvents. In the holopeptide corticotropin, the side chain-side chain effects, as reflected by the titration curves obtained from variations in the aromatic region, support the idea of an helical organization of part of the backbone even in aqueous solution. When going from water to trifluoroethanol corticotropin1-32 undergoes a conformational change which leads to an alpha-helix, following a linear pathway. These results, together with other observations, indicate the possible role of the conformation of corticotropin molecules in their biological life.