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1.
Conformational energy calculations using an Empirical Conformational Energy Program for Peptides (ECEPP) were carried out on the N-acetyl-N′-methylamides of Pro-X, where X = Ala, Asn, Asp, Gly, Leu, Phe, Ser, and Val, and of X-Pro, where X = Ala, Asn, Gly, and Pro. The conformational energy was minimized from starting conformations which included all combinations of low-energy single-residue minima and several standard bend structures. It was found that almost all resulting minima are combinations of low-energy single-residue minima, suggesting that intra residue interactions predominate in determining conformation. The calculations also indicate, however, that inter residue interactions can be important. In addition, librational entropy was found to influence the relative stabilities of some minima. Because of the existence of 10–100 low-energy minima for each dipeptide, the normalized statistical weight of an individual minimum rarely exceeds 0.3, suggesting that these dipeptides have considerable conformational flexibility and exist as statistical ensembles of low-energy structures. The propensity of each dipeptide to form bend conformations was calculated, and the results were compared with available experimental data. It was found that bends are favored in Pro-X dipeptides because ?Pro is fixed by the pyrrolidine ring in a conformation which is frequently found in bends, but that bends are not favored in X-Pro dipeptides because interactions between the X residue and the pyrrolidine ring restrict the X residue to conformations which are not usually found in bends. 相似文献
2.
Conformational energy calculations using an empirical conformatinol energy program for peptides (ECEPP) werer carried out on 16 N-acetyl-N′-methylamides of Ser-X and X- Ser dipeptides, where X = Ala, Asn, Asn, Asp, Gly, Phe, Ser, Thr, and Val, and on Pro-Ser. As with the other dipeptides studied in this serites, intraresidue interactions found to dominate over interresidue interactions in determining conformational properties. The Ser-containing dipeptides (except for those with a pro or Gly residue) were found to have unusually low calculated bend probailities, in disagreement observations on proteins; this discrepancy probably arises becuse of sovent effects (not included in the computations). The Ser-X dipeptides were calculated to have a lower preference for bends than the X-Ser dipeptides. 相似文献
3.
Conformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 20 N-acetyl- N′-methylamides of Gly-X and X-Gly depeptides, where X = Ala, Asn, Asp, Gly, Phe, Ser, Thr, Tyr, Val, and Pro, and also of Leu-Gly. Each depeptde was found to have 25 or more low-energy minima, except Gly-Thr, which had only 11 low-energy minima because of the stable side chian-backbone hydrogen present in all low-energy conformation. As a group, the stble chain-backbone hydrogen bonds present in all low-energy conformations. As a group, the Gly-containing dipeptides were calculated in all low-energy prpensity for formation of bends than the Ala-containing depeptides. The X- Gly dipeptides were calculated to favor bends more than the Gly-X dipeptides, primarlly because of the high stability of the type II bend in X-Gly dipeptides. These results are in agreement with obseved occurrences of bends in the x-ray structures of globular proteins. The calculated conformation properties were found to be in good agreement with experimental results. 相似文献
4.
Integral equation theory is applied to the determination of the intramolecular potential of mean force for the glycine dipeptide, N-acetyl glycyl-N-methylamide, in aqueous solution. The solvated free energy for the dipeptide as a function of the dihedral angles ? and ψ (Ramachandran plot) is determined and compared with the vacuum surface. Conformations forbidden in vacuum are found to be populated in aqueous solution. The results of the glycine dipeptide are compared to a parallel study on the alanine dipeptide. Solvent effects are found to be responsible for the extent of many of glycines properties related to flexibility. 相似文献
5.
Conformational energy calculations were performed on monosaccharide and oligosaccharide inhibitors and substrates of lysozyme to examine the preferred conformations of these molecules. A grid-search method was used to locate all of the low-energy conformational regions for N-acetyl-β-D -glycosamine (NAG), and energy minimization was then carried out in each of these regions. Three stable positions for the N-acetyl group have ben located, in two of which the plane of the amide unit is normal to the mean plane of the pyranosyl ring. Nine local energy minima were located for the —CH2OH group. The positions of the two vicinal cis —OH groups are determined predominantly by interactions with either the —CH2OH or the N-acetyl group. The most stable conformations of β-N-acetylmuramic acid (NAM) were determined from the study of the low-energy conformations of NAG. In the two stable orientations for the D -lactic acid side chain, the O—C—C′ plane (C′ being the carbon atom of the terminal carboxyl group) was found to be normal to the mean plane of the pyranosyl ring. The low-energy positions for the COOH group of NAM are determined mainly by interactions with neighboring groups. The conformational preferences of the α-anomers of NAG and NAM were also explored. The calculated conformation of the N-acetyl group for α-NAG was quite close to that determined by X-ray analysis. Two of the three lowest energy conformations of α-NAM are similar to the corresponding conformations of the β-anomer. A third low-energy structure, which has a hydrogen bond from the NH of the N-acetyl group to the C?O of the lactic acid group, corresponds very closely to the X-ray structure of this molecule. The preferred conformations of the disaccharides NAG–NAG, NAM–NAG and NAG–NAM were also investigated. Two preferred orientations of the reducing pyranosyl ring relative to the nonreducing ring were found for all of these disaccharides, both of which are close to the extended conformation. In one of these conformations, a hydrogen bond can form between the OH group attached to C3 of the reducing sugar and the ring oxygen of the preceding residue. Each conformation can be stabilized further by a hydrogen bond between the CH2OH (donor) of residue i + 1 and the C?O of residue i (acceptor). The interactions that determine conformations for all oligosaccharides containing both NAG and NAM are shown to be exclusively intraresidue and nearest neighbor interactions, so that it is possible to predict all stable conformations of oligosaccharides containing NAG and NAM in any sequence. 相似文献
6.
Conformational energy computations were carried out on collagenlike triple-stranded conformations of several poly(tripeptide)s with the general structure CH3CO? (Gly? X? Y)3? NHCH3. The sequences considered had various amino acid residues in position X or Y of the central tripeptide, with either Pro or Ala as a neighbor, i.e., Gly-X-Pro, Gly-X-Ala, Gly-Pro-Y, and Gly-Ala-Y. Minimum-energy conformations were computed for the side chains, and their distributions were compared for the four sequences. The residues used were Abu (= α-aminobutyric acid), Leu, Phe, Ser, Asp, Asn, Val, Ile, and Thr. The conformational energy of a ? Ch2? CH3 side chain in Abu was mapped as a function of the dihedral angle χ1. Intrastrand interactions with neighboring residues do not affect the conformations of a side chain in position Y, and they have a minor effect on it in the X-Ala sequence, but they strongly restrict the conformational freedom of the side chain in the X-Pro sequence. Conversely, interstrand interactions do not affect side chains in position X, but they strongly restrict the conformational freedom of a side chain in position Y if there is a nearby Pro residue in a neighboring strand. Hydrogen bonds with the backbone can be formed in some conformations of long polar side chains, such as Asp, Asn, or Gln. All amino acid residues can be accommodated in collagen. Because of the interactions mentioned above, steric and energetic constraints can be correlated with observed preferences of certain amino acids for positions X or Y in collagen. Hence, these preferences may be explained, in part, in terms of differences in the conformational freedom of the side chains in the triple-stranded structure. 相似文献
7.
An X-prolyl dipeptidyl aminopeptidase (X-PDAP; EC 3.4.14.5) was identified to be loosely bound on the inner cell membrane fraction of Lactococcus lactis subsp. cremoris nTR. The biosynthesis of X-PDAP was continuously increased before the late-log growth phase of the bacteria. Both Gly-Pro-pNA and Ala-Ala-pNA were hydrolyzed by X-PDAP; the kcat/Km value of the former was about 10-fold that of the latter. The Ki of X-Pro and Pro-X were more specific to X-PDAP than those of X-Ala. The enzyme splitting a dipeptide sequentially from beta-casomorphin as a model catalytic pattern was identified and some properties of the enzyme were further characterized. 相似文献
8.
Several analogues of 5-hydroxytryptophan were tested for their ability to inhibit the binding of serotonin to serotonin-binding protein (SBP), a protein found within serotonergic neurons which has a high affinity for serotonin. An N-substituted dipeptide, N-acetyl-5-hydroxytryptophan-5-hydroxytryptophan amide, was found to be an inhibitor of this binding. The inhibition (50% at 1.0 μM) was specific, since it did not affect other known sites of serotonin binding. The binding of serotonin to its membrane receptor was not affected by the dipeptide (up to 10 μM). Uptake of serotonin by synaptosomes was only slightly affected (9% at 10 μM), and aromatic-L-amino-acid carboxy-lyase(EC 4.1.1.28) and amine: oxygen oxidoreductase (deaminating) (flavin-containing) (EC 1.4.3.4) were not inhibited (10 μM and 5 mM respectively), The peptide was not hydrolyzed by honiogenates of brain or myenteric plexus. The 14C-labelled dipeptide was shown to be taken up by synaptosomes. However, the uptake of the peptide was not affected either by drugs that inhibit serotonin uptake or by serotonin itself although the uptake was abolished by excess 5-hydroxytryptophan. Intraventricular injection of N-acetyl dipeptide caused a biphasic effect depending on dose. Lower doses (10nmol) induced a decrease in serotonin brain levels (40%). Higher doses (300 nmol) caused a 95% increase in serotonin levels. It is suggested that 5-hydroxytryptophyl peptides may be used as potent specific inhibitors of SBP, a storage compartment of serotonin. 相似文献
9.
A model for the simulation of a solution of an alanine dipeptide in water is presented that combines a previous model for bulk water (ST2) with that used in conformational energy studies on small molecules and proteins. The results of a pilot molecular dynamics study indicate that the model leads to reasonable solvent–solute interactions. No evidence is found for substantial changes in the structure or dynamics of the dipeptide in solution as compared to in vacuo. Furthermore, at the elevated temperature examined, there appear to be no significant effects on the dynamics or intermolecular bonding of the water molecules in contact with the solute. 相似文献
10.
B. Picur M. Lisowski I.Z. Siemion 《International journal of peptide research and therapeutics》1998,5(2-3):183-187
Summary We have found that besides the known cyclolinopeptides A (CLA) and B (CLB), there is a new cyclic peptide in linseed mill
cake that we have named CLX. Its composition is very similar to that of CLA, a cyclic peptide with a distinct immunosuppressive
activity. The sequence of this peptide has been established ascyclo(PPFFILLX), where X is a non-proteinaceous amino acid,N-methyl-4-aminoproline. this amino acid substitutes for two amino acid residues of CLA, mimicking a dipeptide moiety with
a nonplanarcis amide bond. The non-proteinaceous amino acid X may mimic a transition state of the peptide bond which exists in such processes
as, e.g., PPIase-catalysedcis/trans amide-Pro bond isomerisation. 相似文献
11.
The adsorption of chiral Gly‐Pro dipeptide on Cu(110) has been characterized by combining in situ polarization modulation infrared reflection absorption spectroscopy (PM‐RAIRS) and X‐ray photoelectron spectroscopy (XPS). The chemical state of the dipeptide, and its anchoring points and adsorption geometry, were determined at various coverage values. Gly‐Pro molecules are present on Cu(110) in their anionic form (NH2/COO−) and adsorb under a 3‐point binding via both oxygen atoms of the carboxylate group and via the nitrogen atom of the amine group. Low‐energy electron diffraction (LEED) and scanning tunneling microscopy (STM) have shown the presence of an extended 2D chiral array, sustained via intermolecular H‐bonds interactions. Furthermore, due to the particular shape of the molecule, only one homochiral domain is formed, creating thus a truly chiral surface. Chirality 27:411–416, 2015. © 2015 Wiley Periodicals, Inc. 相似文献
12.
Serda Kecel-Gunduz Sefa Celik Aysen E. Ozel Sevim Akyuz 《Journal of biomolecular structure & dynamics》2017,35(3):585-602
In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of β-endorphin (glycy-l-glutamine, glycyl-glutamine, beta-endorphin30-31), which is an inhibitory neuropeptide synthesized from beta-endorphin1-31 in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the φ, Ψ, χ dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with ?.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO–LUMO energy gaps were computed using the DFT with the B3LYP/6-31++G(d,p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-l-glutamine dipeptide. 相似文献
13.
Several patients with X chromosome structural abnormalities have been more severely affected clinically than expected. Since bends at Xq13-21 have been associated with inactivation, the authors scored bends retrospectively in 62 patients with X chromosome aneuploidy and 21 cases with structural abnormalities of the X chromosome. They found that patients with 2 X inactivation sites where one X was structurally abnormal had significantly fewer cells with X bends than normal 46,XX. In addition, these patients also showed X bends on the normal X more often than would be expected if non-random X inactivation of the abnormal X chromosome was occurring. Five of the 6 patients with a short or long arm deletion or paracentric inversion of Xq were mentally retarded or had other congenital anomalies not usually associated with Turner syndrome. This suggests to them that these clinical findings may be related to interference with X inactivation patterns in cells with a structurally abnormal X chromosome. 相似文献
14.
Toshifumi Miyazawa Makoto Hiramatsu Takashi Murashima Takashi Yamada 《Biotechnology letters》2002,24(23):1945-1949
The coupling between the carbamoylmethyl ester of an N-protected amino acid or dipeptide (at 25 mM) and an amino acid amide (at 100 mM) was achieved using Aspergillus melleus protease in 1,1,1,3,3,3-hexafluoro-2-propanol/N,N-dimethylformamide (1:1, v/v); the coupling efficiencies were dependent largely on the combination of amino acid residues: e.g. the dipeptide yields after 48 h were for l-Ala + Gly, 100% and for l-Leu + l-Leu, 16%. 相似文献
15.
A study of the 100-MHZ nuclear magnetic resonace spectra in D2O solution was made of a series of linear dipeptides of the types L -phenylalanine-L -and-D -X, and L -phenylalanine-L -and-D -Y, where X comprised a group of amino acid residues with polar side chains (X = glutamine, glutamic acid, arginine, and Nε-acetyllysine) and Y comprised amino acid residues with purely aliphatic side chains (Y = α-aminobutyric acid and norvaline). It was found that regardless of the side chain length, resonances due to the α-methylene protons in the X and Y side chains of the L -Phe-D -Y series consistently exhibited upfield shifts greater than any other protons in these side chains, when compared to the corresponding side chain resonances of the nonaromatic dipeptide series L -Ala-L -X and L -Ala-L -Y. The magnitudes of these shielding effects were consistently and considerably greater for the L -Phe-D -X series than for the L -Phe-D -Y series. An intramolecular complex–formed by association of armatic π-electrons with the positive end of the dipole in the polar side chains—was proposed as one plausible interpretation of the enhanced shielding effects. An increase in temperature from 32 to 70–80° was sufficient to overcome the enhanced shielding attributable to the suggested complex. 相似文献
16.
The concept of bends or chain reversals [nonhelical dipeptide sequences in which the distance R3 (i,i+3) between the Cα atoms of residues i and i+3 is ≦ 7.0 Å] has been extended to define double bends as tripeptide sequences, not in an α-helix, in which two successive distances R3(i,i+3) and R3 (i+1, i+4) are both ≦7.0 Å, with analogous definitions for higher-order multiple bends. A sample of 23 proteins, consisting of 4050 residues, contains 235 single, 58 double, and 11 higher-order multiple bends. Multiple bends may occur as combinations of the “standard” type I, II, and III chain reversals (as well as their mirror images), but usually they require distortions from these well-defined conformations. The frequency of occurrence of amino acids often differs significantly between single and multiple bends. The probability distribution of R3 distances does not differ in single and multiple bends. However, R4 (the distance between the Cα atoms of residues i and i+4) in multiple bends is generally shorter than in tripeptide sequences containing single bends. The value of R4 in many multiple bends is near those for α-helices. In some other multiple bends, R4 is even shorter, indicating that these structures are very compact. The signs of the dihedral angles about the virtual bonds connecting Cα atoms and the values of curvature and torsion, as defined by means of differential geometry, indicate that there is a preference for single and multiple bends to be right-handed (like an α-helical sequence, for example) and that there is a strong tendency to conserve the handedness in both single-bend components of many multiple bends. These often have a strong resemblance to distorted single turns of an α-helix and do not constitute chain reversals. Double bends, in which the signs of two successive virtual-bond dihedral angles differ, have conformations that are very different from an α-helix. They act as chain reversals occuring over three residues. These chain reversals have not been described previously. Multiple bends may play an important role in protein folding because they occur fairly frequently in proteins and cause major changes in the direction of the polypeptide chain. 相似文献
17.
The conformations of 23 terminally blocked dipeptide sequences were examined by conformational energy calculations that included the effects of the aqueous solvent. Starting structures were derived from combinations of minimum-energy conformations of hydrated single residues. Their conformational energies were then minimized using the ECEPP potential (Empirical Conformational Energy Program for Peptides) with hydration included. Short-range interactions dominate in stabilizing the conformations of the hydrated dipeptides. Differences between conformational stabilities of hydrated and unhydrated dipeptides in many cases are due to the competition of solute–water and intramolecular hydrogen bonds. In other cases, perturbation of the hydration shell of the solute by close approach of solute atoms alters conformational preferences. Probabilities of formation of bends were calculated and compared to the corresponding quantities for unhydrated dipeptides and to those calculated from x-ray structures. For bends in dipeptides containing two nonpolar amino acids, computations omitting hydration yield better results. However, better agreement with experimental (x-ray) bend probabilities for dipeptides containing glycine or polar amino acids is obtained only in some sequences when hydration is included. The results are rationalized by the observation that, in proteins, bends containing nonpolar sequences occur on the inside, shielded from the solvent. Bends containing glycine or polar amino acids occur frequently on the surface of the protein, but they are not completely hydrated. 相似文献
18.
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
19.
Summary
N-[(Z)-N-Benzoyl- orN-Boc-(2-fluorophenyl)dehydroalanyl]-(R)-or (S)-phenylalanine esters were synthesized and hydrogenated to give the corresponding dipeptide derivatives with optical yields in the range of 53–87%de using the cationic rhodium complexes of PROPRAPHOS and BPPM. The efficiency of chiral diphosphine ligands as well the effect of the chiral center in the substrate on the catalytic asymmetric induction was studied.Dedicated to Professor Günther Oehme on the occasion of his 60th birthday 相似文献
20.
The chiroptical properties of the cyclic dipeptides cyclo-L -alanyl-L -histidine and cyclo-L -histidinyl-L -histidine have been investigated as a function of molecular conformation. The rotatory strengths of the n-π* transitions of the peptide chromophores and the lowest energy π-π* transitions of the imidazole chromophores have been calculated as a function of the angle of fold of the cyclic dipeptide group and the dihedral angles χ1 and χ2 of the amino acid side chains. The results of this investigation are consistent with the preferred position of the dihedral angle χ1 occurring near 60° in the free base form of cyclo-L -alanyl-L -histidine, and near 180° when the imidazole side chain is protonated. Furthermore, in the case of the free base form of the imidazole group, it is possible that the tautomeric isomer in which Nε is protonated may be more prevalent than the isomer in which Nδ is protonated. 相似文献