Showing papers in "Biopolymers in 1993"
TL;DR: A statistical reference for RNA secondary structures with minimum free energies is computed by folding large ensembles of random RNA sequences, using two binary alphabets, AU and GC, the biophysical AUGC and the synthetic GCXK alphabet.
Abstract: A statistical reference for RNA secondary structures with minimum free energies is computed by folding large ensembles of random RNA sequences. Four nucleotide alphabets are used: two binary alphabets, AU and GC, the biophysical AUGC and the synthetic GCXK alphabet. RNA secondary structures are made of structural elements, such as stacks, loops, joints, and free ends. Statistical properties of these elements are computed for small RNA molecules of chain lengths up to 100. The results of RNA structure statistics depend strongly on the particular alphabet chosen. The statistical reference is compared with the data derived from natural RNA molecules with similar base frequencies. Secondary structures are represented as trees. Tree editing provides a quantitative measure for the distance dt, between two structures. We compute a structure density surface as the conditional probability of two structures having distance t given that their sequences have distance h. This surface indicates that the vast majority of possible minimum free energy secondary structures occur within a fairly small neighborhood of any typical (random) sequence. Correlation lengths for secondary structures in their tree representations are computed from probability densities. They are appropriate measures for the complexity of the sequence-structure relation. The correlation length also provides a quantitative estimate for the mean sensitivity of structures to point mutations.
298 citations
Abstract: The structural preferences of peptides (and depsipeptides) from the achiral MeAib and Hib residues, and the chiral Iva, (alpha Me) Val, (alpha Me) Leu, and (alpha Me) Phe residues, as determined by conformational energy computations, x-ray diffraction analyses, and 1H-nmr and spectroscopic studies, are reviewed and compared with literature data on Aib-containing peptides. The results obtained indicate that helical structures are preferentially adopted by peptides rich in these alpha-amino acids methylated at the alpha-carbon. Intriguing experimental findings on the impact of the chirality of Iva, (alpha Me) Val, and (alpha Me) Phe residues on helix screw sense are illustrated.
225 citations
TL;DR: Partial compressibilities of globular proteins in water are reviewed and possible relaxation contribution to partial compressibility is roughly estimated from comparison of thermodynamic with x‐ray data on protein compressibility.
Abstract: Partial compressibilities of globular proteins in water are reviewed. Contribution of hydrational and of intrinsic compressibilities to experimental partial quantity have been evaluated from ultrasonic data using two independent methods: (a) additive calculation of the hydrational contributions of the surface atomic groups and (b) an analysis of correlation between partial compressibility and molecular surface area. The value (14 ± 3) × 10−6 bar −1 for the isothermal compressibility coefficient of the protein interior at 25°C was obtained as an average value for variety of globular proteins. This value is similar to that of solid organic polymers. Possible relaxation contribution to partial compressibility is roughly estimated from comparison of thermodynamic with x-ray data on protein compressibility. The average compressibility of water in the hydration shell of proteins was found to be 35 × 10−6 bar −1, which is 20% less than that of pure water. © 1993 John Wiley & Sons, Inc.
155 citations
TL;DR: An overview of CD of proline‐rich peptides is reported and it was shown that the addition of increasing amounts of the polyanionic molecule heparin forced a displacement of the conformational equilibrium of those peptides toward higher proportions of thepolyproline II structure when the temperature is raised.
Abstract: An overview of CD of proline-rich peptides is reported. First, structural characteristics, theoretical CD studies, and the biological relevance of polyproline II structure in such peptides are discussed. Second, a CD study of peptides belonging to the repetitive domain of maize glutelin-2, H-(Val-His-Leu-Pro-Pro-Pro)n-OH (n = 3, 5, 8), is described. This series of peptides displayed the CD features of polyproline II structure in water (5°C, pH5). Moreover, it was shown that the addition of increasing amounts of the polyanionic molecule heparin forced a displacement of the conformational equilibrium of those peptides toward higher proportions of the polyproline II structure. In contrast, when the temperature is raised such a structure gradually disappears, leading to more disordered conformations. © 1993 John Wiley & Sons, Inc.
150 citations
TL;DR: An outline of the basic considerations that are under development for the rational design of biologically active peptides and peptidomimetics is given and the application of designer amino acids prepared by asymmetric synthesis to obtain insight into the topographical requirements at δ‐opioid receptors is illustrated.
Abstract: An outline of the basic considerations that are under development for the rational design of biologically active peptides and peptidomimetics is given. The necessary interplay of biophysical, chemical, and biological considerations is emphasized. The importance of properly designed biological assays to provide chemical information analogous to that from biophysical studies is discussed. The development of asymmetric synthesis in conjunction with conformational considerations for the preparation of specialized amino acids and amino acid mimetics is a critical aspect of the approach. The overall approach is illustrated with three examples from our laboratory: (1) the redesign of somatostatin to a highly potent and selective mu-opioid receptor antagonist using conformational and topographical considerations in design and for obtaining insights into the pharmacophor; (2) the use of topographical considerations for obtaining oxytocin antagonists; and (3) the application of designer amino acids prepared by asymmetric synthesis to obtain insight into the topographical requirements at delta-opioid receptors.
149 citations
TL;DR: A new technique is described that removes this limitation and can be used to compute surface shape properties and is useful for efficient rendering and for the display of large‐scale surface features.
Abstract: The representation and characterization of molecular surfaces are important in many areas of molecular modeling. Parametric representations of protein molecular surfaces are a compact way to describe a surface, and are useful for the evaluation of surface properties such as the normal vector, principal curvatures, and principal curvature directions. Simplified representations of molecular surfaces are useful for efficient rendering and for the display of large-scale surface features. Several techniques for representing surfaces by expansions of spherical harmonic functions have been reported, but these techniques require that the radius function is single valued, that is, each ray from an origin inside the surface intersects the surface at one and only one point. A new technique is described that removes this limitation and can be used to compute surface shape properties. © 1993 John Wiley & Sons, Inc.
131 citations
TL;DR: The THP synthetic protocol developed here will allow for the study of both structure and biological activity of specific collagen sequences in homotrimeric and heterotrimer forms.
Abstract: A generally applicable solid-phase methodology has been developed for the synthesis of triple-helical polypeptides incorporating native collagen sequences. Three nascent peptide chains are C-terminal linked through one Nα-amino and two Ne-amino groups of Lys, while repeating Gly-Pro-Hyp triplets induce triple helicity. Different protecting group strategies, including several three-dimensionally orthogonal schemes, have been utilized for the synthesis of four homotrimeric triple-helical polypeptides (THPs) of 79–124 residues, three of which incorporate native type IV collagen sequences. Highly efficient assemblies were achieved by 9-fluorenylmethoxycarbonyl (Fmoc) Nα-amino group protection, in situ 2-(1H-benzotriazole-l-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate mediated couplings, and 1,8-diazabicyclo [5.4.0] undec-7-ene mediated Fmoc group removal. THPs were characterized by Edman degradation sequencing, size-exclusion chromatography, mass spectrometry, reversed-phase high performance liquid chromatography, and CD spectroscopy. THP thermal stabilities ranged from 35 to 59°C, with chain length and Hyp content being the influential factors. Melting temperatures and van't Hoff enthalpies for peptide triple-helical denaturation could be correlated well to Hyp content. The THP synthetic protocol developed here will allow for the study of both structure and biological activity of specific collagen sequences in homotrimeric and heterotrimeric forms. © 1993 John Wiley & Sons, Inc.
97 citations
TL;DR: This report describes the implementation of volumetric and surface‐based techniques for computing shape properties of Cu‐Zu superoxide dismutase and their use in computing the shape properties in protein–protein and protein–ligand interactions.
Abstract: The description of molecular shape is important in the analysis of protein-protein and protein-ligand interactions. We describe volumetric and surface-based techniques for computing shape properties of molecular surfaces. The surface is defined as an isocontour of an approximate electron density function. Each technique can compute several scalar and vector surface properties such as the Gaussian and mean curvature, principal curvatures, and principal curvature directions. Shape properties are derived from the eigenvalues and eigenvectors of a 3 by 3 matrix for each surface point. In the volumetric approach, the matrix is the second derivative of an approximate electron density function. In the surface-based approach, the matrix is the approximate gradient of the surface normal. Derivatives are computed by convolving the density or the surface normals with the derivatives of a Gaussian function. The variance of the Gaussian determines the effective length scale at which the surface is analyzed. Scalar surface properties are displayed as colored dots or shaded triangles, and vector properties are displayed as line segments from each surface point. This report describes the implementation of these procedures and their use in computing the shape properties of Cu-Zu superoxide dismutase.
96 citations
TL;DR: A molecular dynamics simulation was performed on the α‐helix H8‐HC5, the C‐terminal part of myoglobin, under periodic boundary conditions in two different solutions, water and water with 30% 2,2,2‐trifluoroethanol (TFE), at 300 K to investigate the stability of the helix.
Abstract: A molecular dynamics (MD) simulation was performed on the alpha-helix H8-HC5, the C-terminal part of myoglobin (residue 132-153), under periodic boundary conditions in two different solutions, water and water with 30% (v/v) 2,2,2-trifluoroethanol (TFE), at 300 K to investigate the stability of the helix. In both simulations, the initial configuration was a canonical right-handed alpha-helix. In the course of the MD trajectory in water (200 ps), the helix clearly destabilized and began to unfold after 100 ps. In the TFE solution, two stable parts of helical regions were observed after 70 ps of a 200-ps MD simulation, supporting the notion that TFE acts as a structure-forming solvent. (C) 1993 John Wiley & Sons, Inc.
96 citations
TL;DR: An ir spectroscopic analysis of a series of five cyclic pseudo‐hexapeptides known to form β‐turns from previous CD and nmr studies shows that in these cyclic peptides the amide groups involved in β‐ turns give rise to characteristic amide I bands in the range 1638–1646 cm−1, with the exact position depending on the solvent and the nature of the side‐chain substituents.
Abstract: The β-turn represents a structural element frequently encountered in globular proteins. However, in spite of various theoretical and experimental studies the ir signature bands of pure β-turns are still not established beyond doubt. Although considerable information exists now on the ir spectra of β-helical and β-sheet structures, the lack of knowledge concerning turn structures in general, and that of β-turns in particular, presents a major uncertainty in the estimation of global protein secondary structures from ir spectroscopic data. To obtain more specific information about the characteristic amide bands in β-turns, we report herein an ir spectroscopic analysis of a series of five cyclic pseudo-hexapeptides known to form β-turns from previous CD and nmr studies [A. Perczel, M. Hollosi, B. M. Foxman, and G. D. Fasman (1991) Journal of the American Chemical Society, Volume 113, pp. 9772-9784 ]. We show here that in these cyclic peptides the amide groups involved in β-turns that comprise a ten-membered hydrogen-bonded ring (and represent the first H-bond pair in a β-sheet), give rise to characteristic amide I bands in the range 1638–1646 cm−1, with the exact position depending on the solvent and the nature of the side-chain substituents. © 1993 John Wiley & Sons, Inc.
93 citations
TL;DR: Correlations between the ir spectral changes, metal ion binding mode, DNA condensation, and denaturation, as well as conformational features, were established.
Abstract: The interaction of calf thymus DNA with Cu2+and Pb2+ was studied in aqueous solution at pH 6.5 with metal/DNA (P) (P = phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform ir (FTIR) spectroscopy. Correlations between the ir spectral changes, metal ion binding mode, DNA condensation, and denaturation, as well as conformational features, were established.
Spectroscopic evidence has shown that at low metal/DNA (P) molar rations 1/80 and 1/40, copper and lead ions bind mainly to the PO of the backbone, resulting in increased base-stacking interaction and duplex stability. The major copper ion base binding via G-C base pairs begins at r > 1/40, while the lead ion base binding occurs at r > 1/20 with the A-T base pairs. The denaturation of DNA begins at r = 1/10 and continues up to r = 1/2 in the presence of copper ions, whereas a partial destabilization of the helical structure was observed for the lead ion at high metal ion concentration (r = 1/2). Metal-DNA binding also results in DNA condensation. No major departure from the B-family structure was observed, upon DNA interaction with these metal ions. © 1993 John Wiley & Sons, Inc.
TL;DR: In this article, a series of simulations of pancreatic trypsin inhibitor were run using temperature-rescaled molecular dynamics and hybrid Monte Carlo, and it was found that simulations run using hybrid Monte-Carlo equilibrated an order of magnitude faster than those run using the same molecular dynamics.
Abstract: A formal partially dynamical approach to ergodic sampling, hybrid Monte Carlo, has been adapted for the first time from its proven application in quantum chromodynamics to realistic molecular systems. A series of simulations of pancreatic trypsin inhibitor were run using temperature-rescaled molecular dynamics and hybrid Monte Carlo. It was found that simulations run using hybrid Monte Carlo equilibrated an order of magnitude faster than those run using temperature-rescaled molecular dynamics. Certain aspects of improved performance obtained using hybrid Monte Carlo are probably due to the increased efficiency with which this algorithm explores phase space. To discuss this we introduce the notion of “trajectory stiffness”. © 1993 John Wiley & Sons, Inc.
TL;DR: In this article, the authors proposed three methods that enable us to diagonalize large matrices using much less computer memory than the usual harmonic dynamics, which is a straightforward method; it consists of the diagonalization of the Hessian matrix of the potential energy, yielding the vibrational spectrum and the directions of internal motions.
Abstract: Low-frequency collective motions in proteins are generally very important for their biological functions. To study such motions, harmonic dynamics proved most useful since it is a straightforward method; it consists of the diagonalization of the Hessian matrix of the potential energy, yielding the vibrational spectrum and the directions of internal motions. Unfortunately, the diagonalization of this matrix requires a large computer memory, which is a limiting factor when the protein contains several thousand atoms.
To circumvent this limitation we have developed three methods that enable us to diagonalize large matrices using much less computer memory than the usual harmonic dynamics. The first method is approximate; it consists of diagonalizing small blocks of the Hessian matrix, followed by the coupling of the low-frequency modes obtained for each block. It yields the low-frequency vibrational spectrum with a maximum error of 20%. The second method consists, after diagonalizing small blocks, of coupling the high- and low-frequency modes using an iterative procedure. It yields the exact low-frequency normal modes, but requires a long computational time with convergence problems. The third method, DIMB (Diagonalization in a Mixed Basis), which has the best performance, consists of coupling the approximate low-frequency modes with the mass-weighted cartesian coordinates, also using an iterative procedure. It reduces significantly the required computer memory and converges rapidly. The eigenvalues and eigenvectors obtained by this method are without significant error in the chosen frequency range. Moreover, it is a general method applicable to any problem of diagonalization of a large matrix.
We report the application of these methods to a deca-alanine helix, trypsin inhibitor, a neurotoxin, and lysozyme. © 1993 John Wiley & Sons, Inc.
TL;DR: An apolar synthetic octapeptide, Boc-(Ala-Aib)4-OMe, was crystallized in the triclinic space group P1 with cell dimensions a = 11.558 A, b =11.643 A, c = 9.650 A, α = 120.220°, β = 107.000°, γ = 90.430°, V = 1055.889 A3, Z = 1, C34H60O11N8·H2O as mentioned in this paper.
Abstract: An apolar synthetic octapeptide, Boc-(Ala-Aib)4-OMe, was crystallized in the triclinic space group P1 with cell dimensions a = 11.558 A, b = 11.643 A, c = 9.650 A, α = 120.220°, β = 107.000°, γ = 90.430°, V = 1055.889 A3, Z = 1, C34H60O11N8·H2O. The calculated crystal density was 1.217 g/cm3 and the absorption coefficient ϕ was 6.1. All the intrahelical hydrogen bonds are of the 310 type, but the torsion angles, ϕ and ψ, of Ala(5) and Ala(7) deviate from the standard values. The distortion of the 310-helix at the C-terminal half is due to accommodation of the bulky Boc group of an adjacent peptide in the nacking. A water molecule is held between the N-terminal of one peptide and the C-terminal of the other. The oxygen atom of water forms hydrogen bonds with N (1) -H and N (2) -H, which are not involved in the intrahelical hydrogen bonds. The hydrogen atoms of water also formed hydrogen bonds with carbonyl oxygens of the adjacent peptide molecule. On the other hand, 1H-nmr analysis revealed that the octapeptide took an α-helical structure in a CD3CN solution. The longer peptides, Boc-(Ala-Aib)6-OMe and Boc-(Ala-Aib)8-OMe, were also shown to take an α-helical structure in a CD3CN solution. An α-helical conformation of the hexadecapeptide in the solid state was suggested by x-ray analysis of the crystalline structure. Thus, the critical length for transition from the 310- to α-helix of Boc-(Ala-Aib)n-OMe is 8. © 1993 John Wiley & Sons, Inc.
TL;DR: The equilibrium model gives a good description of both the apparent weight average molar masses and the apparent hydrodynamic diameters, when the effect of the insulin concentration is taken into account by including virial effects arising from charge–charge repulsion (Donnan effect).
Abstract: The aggregation properties of zinc-free insulin have been studied using static and dynamic light scattering. The aggregation has been investigated as a function of three parameters, the concentration of sodium chloride (in the range 10-100 mM), the pH value (in the range pH 7.5-10.5), and the insulin concentration (1.8-13.4 mg/mL). The measured homodyne autocorrelation function was used to determine the apparent mean hydrodynamic diameter as well as the apparent weight-averaged molar mass of the insulin species in solution. A method of data analysis was employed, which allows the separation of light scattering contributions from the insulin oligomers and from irrelevant macromolecules and possible impurities present in the sample solutions. Also, a simple phenomenological equilibrium model describing the association of oligomers of insulin is presented. One aspect of this model is that it makes it possible to determine weight average molar masses corrected for virial effects on the Rayleigh ratio. This was necessary because virial effects cannot be isolated and corrected for by dilution since this would change the equilibrium distribution of oligomers. The basis of the model is a positive contribution to Gibbs free energy from charge repulsion depending on the protein charge and the number of monomers in the oligomers, and an assumed constant negative contribution to Gibbs free energy arising from either an entropic gain or hydrogen bonding upon association. The equilibrium model gives a good description of both the apparent weight average molar masses and the apparent hydrodynamic diameters, when the effect of the insulin concentration is taken into account by including virial effects arising from charge-charge repulsion (Donnan effect). The result shows that the association of insulin as a function of pH and ionic strength can be described by an effective charge equal to the charge derived from proton titration reduced by the number of sodium ions binding to insulin. At the lowest pH and highest salt concentration (pH 7.5, 100 mM NaCl, 12 mg/mL insulin), the weight average molar mass is close to that of the hexamer, and at the highest pH and lowest salt concentration (pH 10.5, 10 mM NaCl, 1.9 mg/mL), the weight average molar mass is close to that of the monomer. In all cases, however, a distribution of oligomers is present with a relative Gaussian width of about 30%.(ABSTRACT TRUNCATED AT 400 WORDS)
TL;DR: A new technique for enhancing the solubility of peptides and proteins in organic solvents is described, which involves complexation of polypeptides with stoichiometric amounts of an anionic detergent, such as sodium dodecyl sulfate (SDS).
Abstract: A new technique for enhancing the solubility of peptides and proteins in organic solvents is described. Complexation of polypeptides with stoichiometric amounts of an anionic detergent, such as sodium dodecyl sulfate (SDS), produces diminished aqueous solubility, but enhanced solubility in organic solvents. Consequently, the partitioning of a polypeptide into a nonpolar solvent can be increased by two to four orders of magnitude. In the case of an insulin–SDS complex, the solubility in 1-octanol is more than tenfold greater than in water. In 1-octanol, the native structure of insulin remains intact, as determined by CD spectroscopy, and the thermal denaturation temperature (Tm) is increased by approximately 50°C relative to unfolding in water. Finally, peptides and proteins can be extracted back into an aqueous phase provided the chloride concentration is sufficient to displace bound detergent molecules. © 1993 John Wiley & Sons, Inc.
TL;DR: A new method is developed in which solid state 15N‐nmr spectra obtained from uniaxially aligned molecules placed with the axis of alignment both parallel and perpendicular to the magnetic field are analyzed to yield the orientations of specific molecular bonds.
Abstract: Recent advances in the application of solid state nmr spectroscopy to uniformly aligned biopolymers have opened a window through which to view the detailed structure of biological macromolecules that are unable to be seen with standard techniques for structure determination such as x-ray diffraction. Atomic resolution structural details are obtained from solid state nmr data in the form of bond orientations, which yield the relative positions of specific atoms within the molecule. For static aligned systems such as fibers, in which rapid reorientation about the axis of alignment does not occur, it has generally been necessary to perform trial and error line-shape simulations to extract structural details from nmr spectra arising from a single type of nuclear spin interaction. In the present work, a new method is developed in which solid state 15N-nmr spectra obtained from uniaxially aligned molecules placed with the axis of alignment both parallel and perpendicular to the magnetic field are analyzed to yield the orientations of specific molecular bonds. Analytical expressions are derived that utilize spectral features read from 15N chemical shift anisotropy line shapes to calculate a discrete number of possible orientations for a specific site. The 15N-1H dipolar interaction is employed to further narrow the number of unique orientations possible for a given site. With this method, a neighborhood of possible orientations is quickly determined, and full line-shape simulations within this region of allowed space can be performed to refine the limits of orientation. This technique demonstrates the use of a single type of isotopic label to determine the orientation of a specific molecular group such as a peptide plane within a protein. Results from the application of this method to the Bombyx mori silk fibroin protein provide structural detail that is consistent with currently accepted structural models based on fiber diffraction studies. © 1993 John Wiley & Sons, Inc.
TL;DR: In this article, the authors investigated the conformational effects of modifying the amide group in model dipeptides, including N-methyl amide, N-hydroxy amide and hydrazide.
Abstract: We have investigated the conformational effects of modifying the amide group in model dipeptides. The N-methyl amide ψ[CO-NMe], N-hydroxy amide ψ[CO-N(OH)], N-amino amide ψ[ CO-N (NH2)], retro amide ψ[ NH-CO], reduced amide in the neutral ψ[CH2-NH] and protonated ψ[CH2-N + H2] state, and hydrazide ψ[CO-NH-NH] have been introduced as surrogates of the amide link in pseudopeptide derivatives of the Pro-Gly or Ala-Gly model dipeptides protected on both termini by an amide group. These compounds have been studied in solution by proton nmr and ir spectroscopy, and in the solid state by x-ray diffraction, giving an extended data set of experimental structural and conformational information on pseudopeptide sequences. The conformational effects depend both on the nature and the position of the modified amide link. Some modifications appear to have no intrinsic conformational induction (N-amino and retro amide), but destabilize any local folded structure by hydrogen-bond breaking. Because of the formation of strong intramolecular interactions, others are capable of stabilizing a β-turn (for example protonated reduced amide), or of inducing a particular local conformation such as a β- or γ-like turn (for example N-hydroxy amide). The particular geometry of the cis N-methyl amide and of the “hydrazino” proline favors the formation of a sharp turn of the main chain. All these structural data are of interest to the design of bioactive peptide mimics. © 1993 John Wiley & Sons, Inc.
TL;DR: In this paper, it is suggested that from a microscopic point of view the sol-gel transition phenomena can be explained as a dynamic process in which the low frequency molecular motions are dominant and increase their proportions with the formation of three-dimensional cross-links.
Abstract: 13C-NMR spectroscopic studies have been made on alginate solutions undergoing sol–gel transition induced by four different divalent cations: Ca, Cu, Co, and Mn. From the analysis of nmr spectra and relaxation times, we have found different interaction modes existing between the Ca–alginate systems and the transition metal (Cu, Co, and Mn)–alginate systems. In the Ca–alginate systems, there exists a specific interaction characterized by a strong autocooperative binding between guluronate residues and calcium ions, and all functional groups in guluronate residues are considered to involve the interaction with calcium ions. On the other hand, in transition metal (Cu, Co, and Mn)–alginate systems, sol–gel transition is characterized by a complex formation in which the carboxyl groups in both mannuronate and guluronate residues are coordinated to metal ions. The other functional groups, like hydroxyl groups, do not participate in the binding to metal ions. It is suggested by relaxation time measurements that from a microscopic point of view the sol–gel transition phenomena can be explained as a dynamic process in which the low frequency molecular motions are dominant and increase their proportions with the formation of three-dimensional cross-links. © 1993 John Wiley & Sons, Inc.
TL;DR: Structural changes can be induced in a peptide by selective substitution of coded α‐amino acid residues by noncoded α-aminoacid residues and the consequent production of analogues with modified structure and conformational preferences.
Abstract: Structural changes can be induced in a peptide by selective substitution of coded alpha-amino acid residues by noncoded alpha-amino acid residues and the consequent production of analogues with modified structure and conformational preferences. In this review article we summarize the solid state structural results and the conformational preferences of two classes of "building blocks": (a) the linear and cyclic symmetrically alpha, alpha-disubstituted glycines in which either two identical n-alkyl groups replace the hydrogen atoms of the glycine residue or a cyclic aliphatic side-chain system is formed by linking the two alpha-carbon side chains, respectively; and (b) the beta-alanine residue. Examples, whenever possible, of the use of these residues for the elucidation of the bioactive conformation in the appropriate biological systems will be given.
TL;DR: The secondary structure transformation of β‐lactoglobulin from a predominantly β‐structure into a predominantly α‐helical one, under the influence of solvent polarity changes is reversible.
Abstract: The secondary structure transformation of beta-lactoglobulin from a predominantly beta-structure into a predominantly alpha-helical one, under the influence of solvent polarity changes is reversible. Independent of the alcohol used--methanol, ethanol, or 2-propanol--the midpoints of the observed structural transformation occur around dielectric constant epsilon approximately 60. The structural change destroying the hydrophobic core formed by the beta-barrel structure leads, at room temperature, to the dissociation of the retinol/beta-lactoglobulin complex in the neighborhood of dielectric constant epsilon approximately 50. However, when the dielectric constant of the medium is raised back to epsilon approximately 70 by the decrease of the temperature, both the refolding of BLG into a beta-structure and the reassociation of the retinol/beta-lactoglobulin complex are observed. The esterification of beta-lactoglobulin carboxyl groups has two effects: on the one hand it accelerates the beta-strand alpha-helix transition induced by alcohols. On the other hand, the esterification of beta-lactoglobulin strengthens its interaction with retinol as it may be deduced from the smaller apparent dissociation constant of retinol/methylated beta-lactoglobulin complex. The binding of retinol to modified or unmodified beta-lactoglobulin has no influence (stabilizing or destabilizing) on the folding changes induced by alcohol.
TL;DR: The overcrossing spectrum is proposed as a tool that complements current structural analyses of macromolecules, especially when monitoring structural homologies within a group of related or unrelated polymers.
Abstract: A procedure is developed and applied to characterize the global shape and folding features of the backbone of a chain molecule. The methodology is based on the following concept: the probability of observing a rigid placement of a backbone in 3-space as a projected curve with N overcrossings. The numerical computation of these probabilities allows one to construct the overcrossing spectrum of a macromolecule at a given configuration. Although the spectrum is built from the knowledge of the nuclear geometry of the main-chain atoms, the shape descriptor overlooks local geometrical features (such as distances and contacts) and provides a characterization of essential (topological) features of the overall fold, such as its compactness and degree of entanglement. In contrast with other shape descriptors, the present approach gives an absolute characterization of the configuration considered, and not one that is relative to an arbitrarily chosen reference structure. Moreover, it is possible to discriminate between folding features that otherwise may not be distinguished when using other geometrical or topological global descriptors. The overcrossing spectrum is proposed as a tool that complements current structural analyses of macromolecules, especially when monitoring structural homologies within a group of related or unrelated polymers. In this work, we apply the methodology to the analysis of proteins having the globin fold. The results are compared with those of other proteins exhibiting similar size and number of residues. Some basic properties of the spectra as a function of the chain length are also discussed.
TL;DR: A comparison of the three structures provides a snapshot of the progressive effects of solvation leading to helix unwinding, and the fragility of the heptapeptide helix in solution is demonstrated by nmr studies in CDC13 and (CD3)2SO.
Abstract: The structure of the peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe has been determined in crystals obtained from a dimethylsulfoxide-isopropanol mixture. Crystal parameters are as follows: C38H69N7O10.H20.2C3H7OH, space group P21, a = 10.350 (2) A, b = 26.084 ( 4 ) A, c = 10.395 ( 2 ) A, beta = 96.87 (12), 2 = 2, R = 8.7% for 2686 reflections observed > 3.0 sigma( F) . A single 5 - 1 hydrogen bond is observed at the N-terminus, while two 4 – 1 hydrogen bonds characteristic of a 310-helix are seen in the central segment. The C-terminus residues, Ala ( 6 ) and Leu ( 7) are extended, while Val (5 ) is considerably distorted from a helical conformation. Two isopropanol molecules make hydrogen bonds to the C-terminal segment, while a water molecule interacts with the N-terminus. The structure is in contrast to that obtained for the same peptide in crystals from methanol-water [I. L. Karle, J. L. Flippen-Anderson, K. Uma, and P. Balaram ( 1990) Proteins: Structure, Function and Genetics, Vol. 7, pp. 62-73] in which two independent molecules reveal an almost perfect alpha-helix and a helix penetrated by a water molecule. A comparison of the three structures provides a snapshot of the progressive effects of solvation leading to helix unwinding. The fragility of the heptapeptide helix in solution is demonstrated by nmr studies in CDC13 and ( CD3)2SO. A helical conformation is supported in the apolar solvent CDCl3, whereas almost complete unfolding is observed in the strongly solvating medium ( CD3)2SO.
TL;DR: In this article, the conformation of the iduronate ring in a trisaccharide and as the central residue in a saccharide has been simulated with a 2S0 starting geometry using explicit water and in vacuum with dielectric constants (e) of 1 and 80.
Abstract: Molecular dynamics (MD) simulations of the conformation of the iduronate ring in a methyl glycoside and as the central residue in a trisaccharide have been carried out. Separate simulations were carried out with initial 1C4, 2S0, and 4C1 iduronate ring conformations. Simulations were followed by observing the time development of the Cremer–Pople ring puckering parameters θ,ϕ2. Starting with chair geometries gave trajectories showing only ring oscillations close to the initial geometry. Simulations were performed with a 2S0 starting geometry using explicit water and in vacuum with dielectric constants (e) of 1 and 80, as well as with distance-dependent dielectric functions of 2r and 4r. In both the explicit water simulation and the vacuum (e = 80) simulations, extensive pseudorotational motion was observed in which boat and twist-boat ring conformers interconvert. The overall range of ϕ22 variation in the trisaccharide was about half of that observed in the methyl glycoside. The Haasnoot procedure for calculating H-H coupling constants in saccharides was applied to structures obtained from MD trajectories. Using MD time averaged couplings along with experimental data allowed the relative fractions of chair and boat/twist-boat forms to be derived. © 1993 John Wiley & Sons, Inc.
TL;DR: The results suggest that the protein α‐helices are less stable in films and that the secondary structure may rearrange into β‐sheets at high temperature, and formic acid treatment transformed the secondaryructure of the protein and peptide films into a stable α‐helix or β‐sheet conformations.
Abstract: The solid state secondary structure of myoglobin, RNase A, concanavalin A (Con A), poly(L-lysine), and two linear heterooligomeric peptides were examined by both far-uv CD spectroscopy1 and by ir spectroscopy. The proteins associated from water solution on glass and mica surfaces into noncrystalline, amorphous films, as judged by transmission electron microscopy of carbon-platinum replicas of surface and cross-fractured layer. The association into the solid state induced insignificant changes in the amide CD spectra of all alpha-helical myoglobin, decreased the molar ellipticity of the alpha/beta RNase A, and increased the molar ellipticity of all-beta Con A with no change in the positions of the bands' maxima. High-temperature exposure of the films induced permanent changes in the conformation of all proteins, resulting in less alpha-helix and more beta-sheet structure. The results suggest that the protein alpha-helices are less stable in films and that the secondary structure may rearrange into beta-sheets at high temperature. Two heterooligomeric peptides and poly(L-lysine), all in solution at neutral pH with "random coil" conformation, formed films with variable degrees of their secondary structure in beta-sheets or beta-turns. The result corresponded to the protein-derived Chou-Fasman amino acid propensities, and depended on both temperature and solvent used. The ir and CD spectra correlations of the peptides in the solid state indicate that the CD spectrum of a "random" structure in films differs from random coil in solution. Formic acid treatment transformed the secondary structure of the protein and peptide films into a stable alpha-helix or beta-sheet conformations. The results indicate that the proteins aggregate into a noncrystalline, glass-like state with preserved secondary structure. The solid state secondary structure may undergo further irreversible transformations induced by heat or solvent.
TL;DR: The molecular structure of three protected AzaPro-containing peptides have been determined by x-ray diffraction as mentioned in this paper, and the following geometric characteristics are retained: pyramidal character of the two nitrogen atoms of the pyrazolidine ring; pseudo cis conformation of the urethane (1, 2) or tertiary amide (3) function preceding the Azapro residue; identical absolute values of the Azaproline residue torsion angles (ϕ, ψ) respectively 111° and 23°.
Abstract: The molecular structure of three protected AzaPro-containing peptides have been determined by x-ray diffraction: Z-AzaPro-NHiPr (1; Z: benzyloxycarbonyl), Z-AzaPro-L-Ala-NHiPr (2), and Boc-L-Ala-AzaPro-NHiPr (3; Boc: tert-butyloxycarbonyl). Starting from the key synthon benzyl-azaprolinate, compounds 1, 2, and 3 have been prepared by combined use of liquid phase peptide synthesis method and adequate isocyanates. In all peptides, the following geometric characteristics are retained: (a) pyramidal character of the two nitrogen atoms of the pyrazolidine ring; (b) pseudo cis conformation of the urethane (1, 2) or tertiary amide (3) function preceding the AzaPro residue; (c) identical absolute values of the Azaproline residue torsion angles “ϕ, ψ” respectively 111° and 23°. In compound 2, the two nitrogen atoms of the pyrazolidine ring are R, R but the opposite S, S absolute configurations are observed in compound 3. In the crystal, compound 3 adopts a folded structure similar to a type VI β-turn with a weak intramolecular i + 3 i hydrogen bond, while an extended structure is observed in compound 2. In the light of our findings, in a peptide chain and contrary to the Pro residue, an AzaPro residue should prevent the formation of any type of any type of β-turn with the residue following it but could accommodate a folded structure with a pseudo type VI βturn with the preceding residue. If confirmed, this would be of tremendous importance in the design of biologically active peptides and drugs. © 1993 John Wiley & Sons, Inc.
TL;DR: The preservation of efficient dipolar coupling indicates that the conformational rearrangements that do‐occur on hydration are small and do not involve any significant overall expansion of free volume or weakening of interactions that would increase the reorientational freedom of protein groups.
Abstract: 13C proton decoupled cross-polarization magic-angle spinning nmr spectra of lysozyme are reported as a function of hydration. Increases in hydration level enhance the resolution of the spectra, particularly in the aliphatic region, but has no significant effect on either the rotating frame proton spin–lattice relaxation time or the cross-relaxation time. The enhancement in spectral resolution with hydration is attributed to a decrease in the distribution of isotropic chemical shifts, which reflects a decrease in the distribution of conformational states sampled by the protein. Changes in the distribution of isotropic chemical shifts occur after the addition of water to the charged groups as coverage of the polar side chains and peptide groups takes place. The onset of this behavior occurs at a hydration level of about, 0.1–0.2 g water/g protein and is largely complete at about 0.3 g water/g protein, the same hydration range where changes in the heat capacity are observed. That hydrogen exchange of buried protons can occur at hydration levels significantly lower than those at which changes in the distribution of conformational states are first observed suggests that some motions that mediate exchange are already present in the dry protein. The preservation of efficient dipolar coupling indicates that the conformational rearrangements that do-occur on hydration are small and do not involve any significant overall expansion of free volume or weakening of interactions that would increase the reorientational freedom of protein groups. © 1993 John Wiley & Sons, Inc.
TL;DR: The dehydropeptides examined adopt 310‐helical conformations in solution, and the sense of the helix was found to vary with solvent and temperature, as demonstrated by the sign reversal of the CD spectrum.
Abstract: The peptides Ac-delta Phe-Ala-delta Phe-NH-Me (1), Ac-delta Phe-Val-delta Phe-NH-Me (2), Ac-delta Phe-Gly-delta Phe-Ala-OMe (3), and Boc-Ala-delta Phe-Gly-delta Phe-Ala-OMe (4), containing two dehydro-phenylalanine (delta Phe) residues, were synthesized and the solution structure investigated in various solvents. The nmr and CD measurements indicate that all the dehydropeptides examined adopt 3(10)-helical conformations in solution. The tripeptides 1 and 2 exhibited an intense negative CD exciton couplet, which was assigned to the right-handed screw sense, while the tetrapeptide 3 displayed a CD couplet having opposite sign, which was assigned to the left-handed helical sense. In the pentapeptide 4 the sense of the helix was found to vary with solvent and temperature, as demonstrated by the sign reversal of the CD spectrum. The right-handed sense dominates in hexafluoro-2-propanol, whereas a left-handed helix prevails in chloroform, acetonitrile and methanol. A crucial role for this behavior is likely to be played by the two alanine residues positioned respectively at the head and tail of the sequence, which favor conformations having opposite screw senses.
TL;DR: A pentapeptide containing two dehydrophenylalanines (delta ZPhe) separated by one L-amino acid has been synthesized and its solid state conformation determined as discussed by the authors.
Abstract: alpha,beta-Dehydroamino acids are expected to provide conformational constraint to the peptide backbone. A pentapeptide containing two dehydrophenylalanines (delta ZPhe) separated by one L-amino acid has been synthesized and its solid state conformation determined. The pentapeptide, Boc-Gly-delta ZPhe-Leu-delta ZPhe-Ala-NHCH3, crystallizes from aqueous methanol in the orthorhombic space group P2(1)2(1)2(1). There are four formula units, C35H46N6O7, in a unit cell of dimensions a = 10.155(3), b = 15.175(1), and c = 23.447(2) A, at room temperature. The structure was solved by direct methods program, SIR88, and refined to a final R = 0.038 based on 3049 reflections with I > 2 sigma (I). All the peptide links are trans and the backbone conformation of the pentapeptide can be described as a 3(10)-helix, with mean phi,psi values of -65.1 degrees and -22.8 degrees (the value is averaged over the first four residues). There are four intramolecular 4-->1 type hydrogen bonds characteristic of 3(10)-type helices. In the crystal, the helices are held together by intermolecular N-H...O = C head-to-tail and lateral hydrogen bonding between symmetry related molecules. This mode of packing is similar to the packing motifs observed so often in other oligopeptides that adopt a 3(10)-helical structure.