共查询到20条相似文献,搜索用时 31 毫秒
1.
Vincenzo Barone Francesco Lelj Alfonso Bavoso Benedetto Di Blasio Patrizio Grimaldi Vincenzo Pavone Carlo Pedone 《Biopolymers》1985,24(9):1759-1767
The preferred conformations of N-acetyl-N′-methyl amides of some dialkylglycines have been determined by empirical conformational-energy calculations; minimum-energy conformations were located by minimizing the energy with respect to all the dihedral angles of the molecules. The conformational space of these compounds is sterically restricted, and low-energy conformations are found only in the regions of fully extended and helical structures. Increasing the bulkiness of the substituents on the Cα, the fully extended conformation becomes gradually more stable than the helical structure preferred in the cases of dimethylglycine. This trend is, however, strongly dependent on the bond angles between the substituents on the Cα atom: In particular, helical structures are favored by standard values (111°) of the N-Cα-C′ angle, while fully extended conformations are favored by smaller values of the same angle, as experimentally observed, for instance, in the case of α,α-di-n-propylglycine. 相似文献
2.
Theoretical calculations of the heteronuclear vicinal coupling constant 3J(13C′NCαH) in peptides have been carried out using the Dirac vector model. The results showed an angular dependence for this coupling constant, which can be expressed in the form 3J(13C′NCαH) = A cos2 θ + B cos θ + C, where A, B, and C are constants and θ is related to the torsional angle ? of the peptide backbone. The results of the present calculations are in very good agreement with those obtained using finite perturbation theory at the INDO level of approximation. 相似文献
3.
We use the nmr data concerning the CαH? CβH fragment in eight peptides with rigid side chains to parametrize a Karplus correlation between the vicinal proton Jαβ coupling constant and the dihedral angle θ. When considering molecules containing the fragment CαHα? CβHβHβ′, the three-dimensional structure of the model peptides does not need to be known with accurate precision, since each set of Jαβ and Jαβ′ coupling constants is then related to the coefficients of the Karplus equation. A good correlation is observed with the Karplus equation, which is in substantial agreement with the Jαβ coupling constants reported for rigid as well as rotating Cα? Cβ bonds in peptides. 相似文献
4.
P Gupta-Bhaya 《Biopolymers》1975,14(6):1143-1160
The electron-mediated spin–spin coupling constant J between the amide NH and the α-CH protons in the dipeptide fragment Cα? CO(NH? CαH)R? C′ONH? Cα is dependent on the dihedral angle of rotation (Φ) around the N? C bond. Measurement of J in a series of zwitterionic dipeptides H3N+? CHR1? CONH? CHR2? CO2? (which is conformationally similar to the dipeptide fragment) in TFA solution shows that J is independent of R1, but dependent on the steric bulk of R2. The data are interpreted in terms of a model that assumes that what we measure is an average value of J? a thermal average over all the possible rotamers. The groups R1 and R2 are, in most cases, sterically kept apart by the trans and planar amide bonds, and hence the independence of J of R1. This model is consistent with the theoretical calculations done on the dipeptide fragment. The effect of the structural characteristics of the side chains (e.g., the effect of lengthening and branching the side chains) on the J values in dipeptides is discussed in the light of the existing results of theoretical calculations. Study of 〈J〉 values in tripeptides (C6H5CH2OCONH? CHR1? CONH? CHR2? CO2CH3, essentially three linked peptide units) shows that electrostatic interaction between the two amide bonds modifies the potential energy surface and the 〈J〉 value of a dipeptide subunit in the tripeptides. Also in some cases, direct steric interaction between the two side chains in the two adjacent dipeptide subunits in the tripeptide affects the potential energy surfaces of the individual dipeptide subunits and hence the 〈J〉 values. The influence of the structural characteristics of the side chains of individual amino acids on structure formation at or beyond the dipeptide level is discussed at various points. The J(NH? αCH) values of CH3CONH? CHR? CONH2 and CH3CONH? CHR? CO2CH3 with the same R are quite different for R = valine, leucine, phenylalanine, methionine, but equal for R = glycine. This, coupled with the fact that one of the carboxamide NH resonances has a chemical shift different from its counterpart in simple amides like CH3CONH2 and the other carboxamide NH has the same chemical shift as its counterpart in CH3CONH2, suggest the presence of a hydrogen bond in dipeptide CH3CONH? CHR? CONH2 with carboxamide NH as the donor. Theoretical evidence for two seven-membered hydrogen-bonded rings with the carboxamide NH as donor and the acetyl oxygen as acceptor is summarized. Our data cannot suggest the number of such hydrogen-bonded rings, nor can they conclude the relative proportion of these rings in a particular dipeptide. A discussion of the difficulty of interpretation is presented and the data are discussed under certain simplifying assumptions. 相似文献
5.
A method for generating a complete polypeptide backbone structure from a set of Cα coordinates is presented. Initial trial values of ? and ψ for a selected residue are chosen (essentially from an identification of the conformational region of the virtual-bond backbone, e.g., and α-helical region), and values of ? and ψ for the remaining residues (both towards the N- and C-terminus) are then computed, subject to the constraint that the chain have the same virtual-bond angles and virtual-bond dihedral angles as the given set of Cα coordinates. The conversion from Cα coordinates to full backbone dihedral angles (?,ψ) involves the solution of a set of algebraic equations relating the virtual-bond angles and virtual-bond dihedral angles to standard peptide geometry and backbone dihedral angles. The procedure has been tested successfully on Cα coordinates taken from standard-geometry full-atom structures of bovine pancreatic trypsin inhibitor (BPTI). Some difficulty was encountered with error-sensitive residues, but on the whole the backbone generation was successful. Application of the method to Cα coordinates for BPTI derived from simplified model calculations (involving nonstandard geometry) showed that such coordinates may be inconsistent with the requirement that ?Pro be near ?75°. In such a case, i.e., for residues for which the algebraic method failed, a leastsquares minimizer was then used in conjunction with the algebraic method; the mean-square deviation of the calculated Cα coordinates from the given ones was minimized by varying the backbone dihedral angles. Thus, these inconsistencies were circumvented and a full backbone structure whose Cα coordinates had an rms deviation of 0.26 Å from the given set of Cα coordinates was obtained. 相似文献
6.
Vincent Madison 《Biopolymers》1977,16(12):2671-2692
A survey of over 50 crystal structures indicates that both imino acid and peptide derivatives of proline populate ring conformers consistent with the torsional potentials about single bonds. In both cases, lower barriers for rotation about C? N bonds relative to those about C? C bonds favor smaller values for dihedral angles about the former bonds. In peptides a minimum in the torsional potential about C? N bonds occurs at zero dihedral angle, further favoring small angles. The pyrrolidine-ring dihedral angles of the proline compounds in the solid state obey a cyclopentane-type pseudorotation function. Thus the puckering of the five-membered ring can be quantitatively described by two parameters. Consistent with small dihedral angles about C? N bonds, Cβ and/or Cγ are puckered out of the mean plane of the ring in nearly all of the nonstrained compounds. Utilizing the consistent force-field method of Lifson and coworkers [see A. Warshel, M. Levitt, and S. Lifson (1970) J. Mol. Spectrosc. 33 , 84] the intramolecular energy of five proline peptides was minimized with respect to all internal coordinates. In addition, the energy surface near minima was explored by constraining a particular dihedral angle and reminimizing the energy with respect to all remaining variables. In linear peptides two types of pyrrolidine-ring conformers have identical predicted energies. In the cyclic dipeptide cyclo (Pro-Gly) one of the ring conformers is favored by about 3 kcal/mol, while the cyclic tripeptide cyclo(Pro-Gly-Gly) favors the other conformer by a comparable margin. In agreement with observations in the solid state and in solution, Cβ and/or Cγ are puckered in the predicted conformers. A correlation between proline Φ and the details of the puckered conformation was predicted and found to match precisely conformers observed in crystals. For the diamides N-acetyl-L -proline-N′-methyl-amide and N-acetyl-L -proline-N′,N′-dimethylamide (AcProMe2A) 30% and 60% cis acetyl peptide bonds were predicted in good agreement with observations in nonpolar solvents for the respective compounds. The conformational distributions with respect to proline Ψ are also in accord with experimental observations. For AcProMe2A, a model for a -Pro-Pro-sequence in a peptide chain, this study is the first to predict stable conformers for proline Ψ either ca. ?50° or 140° for both cis and trans peptides. 相似文献
7.
Glenn L. Butterfoss Eugene F. DeRose Scott A. Gabel Lalith Perera Joseph M. Krahn Geoffrey A. Mueller Xunhai Zheng Robert E. London 《Journal of biomolecular NMR》2010,48(1):31-47
Methionine residues fulfill a broad range of roles in protein function related to conformational plasticity, ligand binding,
and sensing/mediating the effects of oxidative stress. A high degree of internal mobility, intrinsic detection sensitivity
of the methyl group, and low copy number have made methionine labeling a popular approach for NMR investigation of selectively
labeled protein macromolecules. However, selective labeling approaches are subject to more limited information content. In
order to optimize the information available from such studies, we have performed DFT calculations on model systems to evaluate
the conformational dependence of 3
J
CSCC, 3
J
CSCH, and the isotropic shielding, σiso. Results have been compared with experimental data reported in the literature, as well as data obtained on [methyl-13C]methionine and on model compounds. These studies indicate that relative to oxygen, the presence of the sulfur atom in the
coupling pathway results in a significantly smaller coupling constant, 3
J
CSCC/3
J
COCC ~ 0.7. It is further demonstrated that the 3
J
CSCH coupling constant depends primarily on the subtended CSCH dihedral angle, and secondarily on the CSCC dihedral angle. Comparison
of theoretical shielding calculations with the experimental shift range of the methyl group for methionine residues in proteins
supports the conclusion that the intra-residue conformationally-dependent shift perturbation is the dominant determinant of
δ13Cε. Analysis of calmodulin data based on these calculations indicates that several residues adopt non-standard rotamers characterized
by very large ~100° χ3 values. The utility of the δ13Cε as a basis for estimating the gauche/trans ratio for χ3 is evaluated, and physical and technical factors that limit the accuracy of both the NMR and crystallographic analyses are
discussed. 相似文献
8.
Jozef Hritz Tilman Läppchen Chris Oostenbrink 《European biophysics journal : EBJ》2010,39(12):1573-1580
The FtsZ protein is a self-polymerizing GTPase that plays a central role in bacterial cell division. Several C8-substituted
GTP analogs are known to inhibit the polymerization of FtsZ by competing for the same binding site as its endogenous activating
ligand GTP. Free energy calculations of the relative binding affinities to FtsZ for a set of five C8-substituted GTP analogs
were performed. The calculated values agree well with the available experimental data, and the main contribution to the free
energy differences is determined to be the conformational restriction of the ligands. The dihedral angle distributions around
the glycosidic bond of these compounds in water are known to vary considerably depending on the physicochemical properties
of the substituent at C8. However, within the FtsZ protein, this substitution has a negligible influence on the dihedral angle
distributions, which fall within the narrow range of −140° to −90° for all investigated compounds. The corresponding ensemble
average of the coupling constants 3
J(C4,H1′) is calculated to be 2.95 ± 0.1 Hz. The contribution of the conformational selection of the GTP analogs upon binding
was quantified from the corresponding populations. The obtained restraining free energy values follow the same trend as the
relative binding affinities to FtsZ, indicating their dominant contribution. 相似文献
9.
Semiempirical quantum chemical calculations were carried out using the CNDO/2 and the INDO methods on the model compound cis-N-methylacetamide in order to get an insight into the problem of possible nonplanar distortions of the cis-peptide unit. In addition, the crystal structure data of cyclic peptides containing cis-peptide units were analyzed. These studies have indicated that the dihedral angles θN and Δω are correlated approximately by the relation Δω = ?θN, whereas θC is small and is uncorrelated with Δω, as was found in the case of the trans-peptide unit. Both theory and crystal data suggest that out-of-plane distortions at the nitrogen atom of the peptide unit were quite likely to occur and should be included in the conformational calculations. The average geometry for the planar cis-peptide unit has also been obtained from the observed examples. 相似文献
10.
The self-association of N-acetylglycine N,N-dimethylamide, N-acetyl-L -valine N,N-dimethylamide, and N-acetyl-L -phenylalanine N,N-dimethylamide in carbon tetrachloride was investigated by using ir and 1H-nmr methods. It was concluded from ir measurements that the associated species is the dimer formed as a result of the simultaneous formation of two intermolecular hydrogen bonds. This is supported by the results of 1H-nmr measurements. Thermodynamic quantities for the association were determined from the temperature and concentration dependence of the NH proton chemical shifts of the sample solutions. Compared with the Gly derivative, L -Val and L -Phe derivatives have larger values of ?ΔH for association, which shows good correlation with ΔvNH values, the difference between the maxima of the monomer and dimer bands, obtained from ir spectra. This is due to the less stable monomer conformation and to the stronger intermolecular hydrogen bonding of the dimers in L -Val and L -Phe derivatives. The line shapes of both methyl proton resonances of L -Val residue and methylene proton resonances of L -Phe residue were found to vary with concentration and temperature of the sample solutions. These data indicate that the rotation about the Cα—Cβ bond is restricted by the steric hindrance present in the associated dimers. All these experimental results can be related to the fact that L -Val and L -Phe derivatives have a warped framework because of the bulky side chains, whereas the Gly derivative has a planar framework. 相似文献
11.
The proton magnetic resonance spectrum of thyrotropin releasing factor (TRF) in solution in deuterium oxide and deuterated dimethylsulfoxide (DMSO–d6) has been analyzed. Two forms differing in cis–trans isomerism about the His-Pro peptide bond are observed. From the temperature dependence of chemical shift of the amide protons, it is concluded that TRF in DMSO–d6 does not contain intramolecular hydrogen bonds. Measurement of NH? CαH coupling constant provides an estimate of the histidine dihedral angle ?. Structural information about the histidine side-chain is deduced from CαH? CβH coupling constants and from the nonequivalence of the two prolyl δ-protons. In DMSO–d6, there is evidence for a tautomeric equilibrium corresponding to an exchange of imidazole proton between the two nitrogen atoms N-δ and N-ε. In water, the N-εH tautomer is found to be the predominant tautomeric form of the imidazole ring. These results in combination with energy calculation, vibrational analysis, and carbon nmr studies allow the determination of the conformationof TRF. 相似文献
12.
E. Benedetti V. Barone A. Bavoso B. Di Blasio F. Lelj V. Pavone C. Pedone G. M. Bonora C. Toniolo M. T. Leplawy K. Kaczmarek A. Redlinski 《Biopolymers》1988,27(3):357-371
Conformational energy computations on a derivative and a homo-dipeptide of Cα,α-diethylglycine were performed. In both cases the N- and C-terminal groups are blocked as acetamido and methylamido moieties, respectively. It was found that the Cα,α-diethylglycine residues are conformationally restricted and that the minimum energy conformation corresponds to the fully extended C5 structure when the N? Cα? C′ bond angle is smaller than 108° (as experimentally observed). The results of the theoretical analysis are in agreement with the crystal-state structural propensity of the complete series of N-trifluoroacetylated homo-peptides of this Cα,α-dialkylated residue from monomer to pentamer, determined by x-ray diffraction and also described in this work. Interestingly, for the first time, a crystallographically planar peptide backbone was observed (in the protected tripeptide). A comparison with peptides of Cα,α-dimethylglycine, Cα-methyl, Cα-ethylglycine, and Cα,α-di-n-propylglycine indicates that the fully extended conformation becomes more stable than the helical structures when both amino acid side-chain Cβ atoms are substituted. 相似文献
13.
Schmidt JM 《Journal of biomolecular NMR》2007,37(4):287-301
The standard Karplus equation for calculating 3
J coupling constants from any given dihedral angle requires three empirical coefficients be determined that relate to the magnitudes
of three modes of the angle dependency of 3
J. Considering cosine modes only (bimodal, unimodal and baseline component), Karplus curves are generally symmetric with respect
to the sign of the angle argument. Typically, their primary and secondary maxima differ in amplitude, whereas the two minima
are of equal depth. However, chiral molecular topologies, such as those surrounding the main-chain and side-chain torsions
in amino-acid residues, preclude, as regards substituent positioning, exact mirror-image conformations from being formed—for
any given torsion-angle value. It is therefore unlikely that 3
J couplings assume identical values for the corresponding positive and negative dihedral angles. This suggests that a better
empirical fit of the torsion-angle dependency of 3
J could be obtained when removing the constraint of symmetrically identical coupling constants. A sine term added to the Karplus
equation allows independent modelling of both curve minima typically located near dihedral-angle values of +90° and −90°.
Revisiting an extensive 3
J coupling dataset previously recorded to determine the side-chain torsions χ1 in the protein flavodoxin, the asymmetric Karplus model accomplishes a more accurate fit to the experimental data. Asymmetries
revealed in the angle dependencies exceed the experimental precision in determining 3
J. Accounting for these effects helps improve molecular models.
Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
14.
Dermenkephalin, H-Tyr-(D ) Met-Phe-His-Leu-Met-Asp-NH2, a highly potent and selective δ-opioid peptide isolated from frog skin, was studied in DMSO-d6 solution by two-dimensional nmr spectroscopy, including the determination of NH temperature coefficients, the evaluation of 3J coupling constants from phase-sensitive correlated spectroscopy (COSY) and the volumes of nuclear Overhauser effect (NOE) correlations. The two-dimensional NOE spectroscopy (NOESY) spectrum of dermenkephalin revealed sequential, medium-, and long-range effects. To put this information on a quantitative basis, special attention was devoted to J cross-peak suppression, quantification of the NOE volumes and analysis of the overlaps, normalization of the NOEs against diagonal peaks and Hββ′ geminal interactions. Although most of the dihedral angles deduced from the 3JNα coupling constants together with several Niαi and αiNi + 1 NOEs pointed to a partially extended peptide backbone, several Ni Ni + 1 NOEs and βi Ni + 1 interactions argued in favor of a folded structure. Moreover, several long-range correlations of strong intensities were found that supported a close spatial proximity between the side chains of D -Met2 and Met6, Tyr1 and His4, Tyr1 and Asp7, and His4 and the C-terminal amide group. In Phe, the g? rotamer in the side chain is deduced from the 3Jαβ coupling constants and αβ and Nβ NOE correlations. Whereas the amide proton dependency was not indicative of stable hydrogen bonds, the nonuniform values of the temperature coefficient may reflect an equilibrium mixture of folded and extended conformers. The overall data should provide realistic starting models for energy minimization and modelization studies. © 1993 John Wiley & Sons, Inc. 相似文献
15.
C. Toniolo G. M. Bonora A. Bavoso E. Benedetti B. Di Blasio V. Pavone C. Pedone V. Barone F. Lelj M. T. Leplawy K. Kaczmarek A. Redlinski 《Biopolymers》1988,27(3):373-379
The conformational preferences of the N-trifluoroacetylated homo-peptides of Cα,α-diethylglycine from monomer to pentamer in chloroform solution were determined by using ir absorption and 1H-nmr. Intramolecular hydrogen bonding was found to be the dominant factor for all NH groups. The likely absence of a conformational transition upon increasing main-chain length, and the remarkable stability to dilution, heating, and addition of perturbing agents, are additional relevant findings of this study. These results are in agreement with those of the fully extended, C5-conformation-forming homo-peptides from the higher homolog Cα,α-di-n-propylglycine, but contrast dramatically to those of the homo-peptides from the lower homolog Cα,α-dimethylglycine, which have been shown to adopt the 310-helical structure. 相似文献
16.
A coupling constant-dihedral angle correlation for the H? Cα? Cβ? H system of amino acid residues in peptides has been derived from a set of model compounds covering the full range of dihedral angles. The expression obtained, J = 11.0 cos2 θ ?1.4 cos θ + 1.6 sin2θ, is close to those already used in pmr studies of peptide conformation, and provides a firmer foundation for them. A factor limiting the precision of this and other “Karplus relations” is illustrated. 相似文献
17.
Conformational analysis of N-methylamide of pyroglutamic acid has been performed by theoretical energy calculations and experimental physical techniques, namely, laser Raman spectroscopy and depolarized Rayleigh scattering. The two theoretically predicted conformations are evidenced in crystalline state (ψ1 = +169°) and in aqueous solution (ψ1 ? ?20°). This study confirms the interest of a careful vibrational analysis of peptides and N-deuterated derivatives for providing an estimate of the dihedral angle ψ. The relationship between amide III frequency and ψ values is emphasized. 相似文献
18.
Kaiwan Gan Peter Alexander James M. Coxon A. John McKinnon Gillian H. Worth 《Biopolymers》1997,41(4):367-379
A multiple regression analysis has established a nonlinear relationship between the backbone dihedral angles and the Cα coordinates obtained from the x-ray crystal structures of 14 proteins. The regression equations have been applied to predict specific dihedral angles of each residue in the backbone of 24 proteins. Overall this method (Nonlinear Regression Distance Torsion) predicts values of ϕ and ψ within a ±45° window of those found in the x-ray structure with an accuracy of 94 and 91% and within a ±30° window of 88 and 81%. Two methods for the assignment of motif from Cα coordinates are reported. For the first method, motif is assigned from the dihedral angles predicted using the regression equations. By the second method, motif of the ith residue is assigned from the distance Cαi-1 to Cαi+2 (v6) and torsional angle Cαi-1, Cαi, Cαi+1, Cαi+2 (v13). For the 24 proteins, 23.7% of the residues by the former method and 19.6% by the latter method are assigned differently than in the Protein Data Bank. © 1997 John Wiley & Sons, Inc. 相似文献
19.
The results of the molecular dynamics simulations of the complexes of α-cyclodextrin-l-phenylalanine and β-cyclodextrine- L- phenylalanine in vacuo and in aqueous solution are presented. The trajectories of the insertion angle, rotation of the aromatic ring of the phenylalanine inside the macrocycle and the dihedral angle χ2 (Cα–Cβ–Cγ–CD2) describing the relative movement of the aromatic ring with respect to the polar region give detailed information of the dynamics of the complexes. It is found that the complex with α-cyclodextrin in water is not stable, in agreement with experimental data, while in all other situations studied the complex is stable within the computational limits. Comparing the different cases and the experimental evidence it comes out that a simulation of the complexes without an explicit treatment of the solvent gives unreliable results. 相似文献
20.
The chiroptical properties of S-proline conformational isomers are examined on a theoretical model in which electronic wave functions are obtained from semiempirical molecular orbital calculations. The CNDO/S molecular orbital model is used to perform SCF-MO calculations on ground state electronic structure and excited states are constructed in the virtual orbital-configuration interaction approximation. Electronic rotatory strengths and dipole strengths are calculated directly from the complete (but approximate) molecular electronic wave functions. Zwitterionic, cationic, and anionic S-proline structures are studied twotypes of conformational variables are represented in the calculations: (1) pyrrolidine ring conformation; and (2) rotation about the Cα-COO? bond. Rotatory strengths are found to be somewhat sensitive to rotational isomerism about the Cα-COO? bond, but are found to be rather insensitive to conformational changes within the pyrrolidine ring. The CD spectrum of zwitterionic S-proline down to ~160 nm appears to be well accounted for by the theoretically calculated results if conformational preferences with respect to rotation about the Cα-COO? bond can be assumed to exist in solution media. Furthermore, spectra-structure correlations are offered for the anionic and cationic forms of S-proline in solution. 相似文献