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1.
Abstract: We report the observation of continuous turns in proteins which comprise individual γ‐turns or β‐turns or both that are situated immediately one after the other along the polypeptide chain. The continuous turns were identified from a representative data set of three‐dimensional protein crystal structures. The γβ/βγ, γγ and ββ continuous turns represent peptides of varying amino acid residue lengths and conformations. The continuous turns frequently observed in proteins were: γβ, between a coil and a strand; βγ, between a helix and a strand; γγ, between coils; and ββ, either between a strand and a coil or between strands or coils. We determined the statistically significant amino acid residue preferences at individual positions in the turn, calculated amino acid positional potentials and analyzed main chain hydrogen bonds and side‐chain interactions likely to stabilize the continuous turns. The data on continuous turns have been integrated in the database of structural motifs in proteins (DSMP) on our web server at ( http://www.cdfd.org.in/dsmp.html ). This is useful to make queries on sequences compatible with different continuous turns.  相似文献   

2.
Abstract: We evaluated the prediction of β‐turns from amino acid sequences using the residue‐coupled model with an enlarged representative protein data set selected from the Protein Data Bank. Our results show that the probability values derived from a data set comprising 425 protein chains yielded an overall β‐turn prediction accuracy 68.74%, compared with 94.7% reported earlier on a data set of 30 proteins using the same method. However, we noted that the overall β‐turn prediction accuracy using probability values derived from the 30‐protein data set reduces to 40.74% when tested on the data set comprising 425 protein chains. In contrast, using probability values derived from the 425 data set used in this analysis, the overall β‐turn prediction accuracy yielded consistent results when tested on either the 30‐protein data set (64.62%) used earlier or a more recent representative data set comprising 619 protein chains (64.66%) or on a jackknife data set comprising 476 representative protein chains (63.38%). We therefore recommend the use of probability values derived from the 425 representative protein chains data set reported here, which gives more realistic and consistent predictions of β‐turns from amino acid sequences.  相似文献   

3.
Abstract: Crystal structure analysis of a model peptide: Boc‐β‐Ala‐Aib‐β‐Ala‐NHCH3 (β‐Ala: 3‐amino propionic acid; Aib: α‐aminoisobutyric acid) revealed distinct conformational preferences for folded [φ≈136°, µ ≈ ?62°, ψ ≈100°] and semifolded [φ ≈ 83°, µ ≈ ?177°, ψ ≈ ?117°] structures of the N‐ and C‐terminus β‐Ala residues, respectively. The overall folded conformation is stabilized by unusual Ni···H‐Ni+1 and nonconventional C–H···O intramolecular hydrogen bonding interactions.  相似文献   

4.
Abstract: A model peptide AAGDYY‐NH2 (B1), which is found to adopt a β‐turn conformation in the TEM‐1 β‐lactamase inhibitor protein (BLIP) in the TEM‐1/BLIP co‐crystal, was synthesized to elucidate the mechanism of its β‐turn formation and stability. Its structural preferences in solution were comprehensively characterized using CD, FT‐IR and 1H NMR spectroscopy, respectively. The set of observed diagnostic NOEs, the restrained molecular dynamics simulation, CD and FT‐IR spectroscopy confirmed the formation of a β‐turn in solution by the model peptide. The dihedral angles [(φ3, ?3) (φ4, ?4)] of [(?52°, ?32°) (?38°, ?44°)] of Gly‐Asp fragment in the model peptide are consistent with those of a type III β‐turn. In a conclusion, the conformational preference of the linear hexapeptide B1 in solution was determined, and it would provide a simple template to study the mechanism of β‐turn formation and stability.  相似文献   

5.
Mimetics of β‐turn structures in proteins have been used to calibrate the relative reactivities toward deamidation of asparagine residues in the two central positions of a β‐turn and in a random coil. N‐Acetyl‐Asn‐Gly‐6‐aminocaproic acid, an acyclic analog of a β‐turn mimic undergoes deamidation of the asparaginyl residue through a succinimide intermediate to generate N‐acetyl‐Asp‐N‐Gly‐6‐aminocaproic acid (6‐aminocaproic acid, hereafter Aca) and N‐acetyl‐l ‐iso‐aspartyl (isoAsp)‐Gly‐Aca (pH 8.8, 37 °C) ≈ 3‐fold faster than does the cyclic β‐turn mimic cyclo‐[L‐Asn‐Gly‐Aca] with asparagine at position 2 of the β‐turn. The latter compound, in turn, undergoes deamidation ≈ 30‐fold faster than its positional isomer cyclo‐[Gly‐Asn‐Aca] with asparagine at position 3 of the β‐turn. Both cyclic peptides assume predominantly β‐turn structures in solution, as demonstrated by NMR and circular dichroism characterization. The open‐chain compound and its isomer N‐acetyl‐Gly‐Asn‐Aca assume predominantly random coil structures. The latter isomer undergoes deamidation 2‐fold slower than the former. Thus the order of reactivity toward deamidation is: asparagine in a random coil ≈ 3× asparagine in position 2 of a β‐turn ≈ 30× asparagine in position 3 of a β‐turn.  相似文献   

6.
αA‐Crystallin can function like a molecular chaperone. We recently reported that the αA‐crystallin sequence, KFVIFLDVKHFSPEDLTVK (peptide‐1, residues 70–88) by itself possesses chaperone‐like (anti‐aggregating) activity during a thermal denaturation assay. Based on the above data we proposed that the peptide‐1 sequence was the functional site in αA‐crystallin. In this study we investigated the specificity of peptide‐1 against γ‐crystallin aggregation in the presence of H2O2 and CuSO4. Peptide‐1 was able to completely protect against the oxidation‐induced aggregation of γ‐crystallin. Removal of N‐terminal Lys or the replacement of Lys with Asp ( D FVIFLDVKHFSPEDLTVK, peptide‐2) did not alter the anti‐aggregation property of peptide‐1. However, deletion of KF residues from the N‐terminus of peptide‐1 resulted in a significant loss of its anti‐aggregation property. Bio‐gel P‐30 size‐exclusion chromatography of γ‐crystallin incubated with peptide‐2 under oxidative conditions revealed that a major portion of the peptide elutes in the void volume region along with γ‐crystallin, suggesting the binding of the peptide to the protein. Peptide‐1 and ‐2 were also able to prevent the UV‐induced aggregation of γ‐crystallin. These data indicate that the same amino acid sequence in αA‐crystallin is likely to be responsible for suppressing the heat‐denatured, oxidatively modified and UV‐induced aggregation of proteins.  相似文献   

7.
Abstract: Replacement of Phe3 in the endogenous δ‐opioid selective peptide deltorphin I with four optically pure stereoisomers of the topographically constrained, highly hydrophobic novel amino acid β‐isopropylphenylalanine (β‐iPrPhe) produced four pharmacologically different deltorphin I peptidomimetics. Radiolabeled ligand‐binding assays and in vitro biological evaluation indicate that the stereoconfiguration of the iPrPhe residue plays a crucial role in determining the binding affinity, bioactivity and selectivity of [β‐iPrPhe3]deltorphin I analogs: a (2S,3R) configuration of the iPrPhe3 residue in [β‐iPrPhe3]deltorphin I provided the most desirable biological properties with binding affinity (IC50 = 2 n m ), bioassay potency (IC50 = 1.23 n m in MVD assay) and exceptional selectivity for the δ‐opioid receptor over the µ‐opioid receptor (30 000). Further conformational studies based on two‐dimensional NMR and computer‐assisted molecular modeling suggested a model for the possible bioactive conformation in which the Tyr1 and (2S,3R)‐β‐iPrPhe3 residues adopt trans side‐chain conformations, and the linear peptide backbone favors a distorted β‐turn conformation.  相似文献   

8.
Abstract: The NMR structural analysis of two fertilinβ mimics cyclo(EC2DC1)YNH2, 1 , and cyclo(D2EC2D1C1)YNH2, 2 is described. Both of these mimics are moderate inhibitors of sperm?egg binding with IC50 values of 500 µm in a mouse in vitro fertilization assay. For peptide 1 , the optimized conformations that best match the NMR data have a pseudo‐type II′β‐turn with the linker and Glu at the i+1 and i+2 positions, respectively. The EC2D1C1 sequence is in a nonclassical (type IV) β‐turn. For peptide 2 , the conformation that best matches the NMR data has two turns: a pseudo‐type II′β‐turn in the D2EC2D1 sequence followed by a nonclassical β‐turn in the EC2D1C1 sequence. The Cβ?Cβ distance between E and D1 in peptide 1 is 9.1 Å, in peptide 2 , it is 7.7 Å. Thus, one possibility for the high IC50 values of these cyclic peptides is that the acidic residues are not constrained to a sufficiently tight turn, and thus much entropy must still be lost upon binding to the α6β1 integrin. This explains why the cyclic peptides are the same as linear peptides at inhibiting sperm?egg binding.  相似文献   

9.
Abstract: In a previous study we designed a 20‐residue peptide able to adopt a significant population of a three‐stranded antiparallel β‐sheet in aqueous solution (de Alba et al. [1999]Protein Sci. 8, 854–865). In order to better understand the factors contributing to β‐sheet folding and stability we designed and prepared nine variants of the parent peptide by substituting residues at selected positions in its strands. The ability of these peptides to form the target motif was assessed on the basis of NMR parameters, in particular NOE data and 13Cα conformational shifts. The populations of the target β‐sheet motif were lower in the variants than in the parent peptide. Comparative analysis of the conformational behavior of the peptides showed that, as expected, strand residues with low intrinsic β‐sheet propensities greatly disfavor β‐sheet folding and that, as already found in other β‐sheet models, specific cross‐strand side chain–side chain interactions contribute to β‐sheet stability. More interestingly, the performed analysis indicated that the destabilization effect of the unfavorable strand residues depends on their location at inner or edge strands, being larger at the latter. Moreover, in all the cases examined, favorable cross‐strand side chain–side chain interactions were not strong enough to counterbalance the disfavoring effect of a poor β‐sheet‐forming residue, such as Gly.  相似文献   

10.
Abstract: We predicted γ‐turns from amino acid sequences using the first‐order Markov chain theory and enlarged representative data sets corresponding to protein chains selected from the Protein Data Bank (PDB). The following data sets were used for training and deriving the probability values: (1) an initial data set containing 315 protein chains comprising 904 γ‐turns and (2) a later data set in order to include new entries in the PDB, containing 434 protein chains and comprising 1053 γ‐turns. By excluding 93 protein chains that were common to these two training data sets, we generated two mutually exclusive data sets containing 222 and 341 protein chains for testing our predictions. Applying amino acid probability values derived from training data sets on to testing data sets yielded overall prediction accuracies in the range 54–57%. We recommend the use of probability values derived from the data set comprising 315 protein chains that represents more γ‐turns and also provides better predictions.  相似文献   

11.
Abstract: Neuropeptide γ belongs to tachykinin families which have a common C‐terminal amino acid sequence (Phe‐X‐Leu‐Met‐NH2) and which induce various biological responses including salivation, hypotension, and contraction of gastrointestinal, respiratory, and urinary smooth muscle. In the present study, we present the solution structures of neuropeptide γ (NPγ) from gold fish (G‐NPγ) and mammalian NPγ (M‐NPγ), as determined by nuclear magnetic resonance (NMR) spectroscopy in 50% trifluoroethanol (TFE)/water (1 : 1, v/v) solution and 200 mm sodium dodecyl sulfate (SDS) micelles. In aqueous TFE solution, G‐NPγ has a α‐helical conformation in the region of His12–Met21 and a short helix in the N‐terminal region, and has a β‐turn from Arg9 to Arg11 in between. In aqueous TFE solution, M‐NPγ also has α‐helical conformations both in the C‐terminal region and the N‐terminal region and a β‐turn from His9 to Arg11 in between. In SDS micelle, the structure of G‐NPγ contains a stable α‐helix from His12 to Met21 and a β‐turn from Arg9 to Arg11, while M‐NPγ has a short helix from Ser16 to Met21. The region from His12 to Met21 corresponds to the amino acid sequence of neurokinin A. Neuropeptide γ may act as a precursor of neurokinin A and the post‐translational processing of this peptide involves the enzymatic attack of the basic β‐turn region from residue 9 to residue 11 in the middle. From our relaxation study, it could be suggested that in fish system G‐NPγ induces the biological actions corresponding to those of substance P in mammalian system. The structures of G‐NPγ and M‐NPγ contain α‐helical structures at the C‐terminus and this helix seems to promote the affinity for NK1 and/or NK2 receptor.  相似文献   

12.
Abstract: We describe here a systematic study to determine the effect on secondary structure of d ‐amino acid substitutions in the nonpolar face of an amphipathic α‐helical peptide. The helix‐destabilizing ability of 19 d ‐amino acid residues in an amphipathic α‐helical model peptide was evaluated by reversed‐phase HPLC and CD spectroscopy. l ‐Amino acid and d ‐amino acid residues show a wide range of helix‐destabilizing effects relative to Gly, as evidenced in melting temperatures (ΔTm) ranging from ?8.5°C to 30.5°C for the l ‐amino acids and ?9.5°C to 9.0°C for the d ‐amino acids. Helix stereochemistry stability coefficients defined as the difference in Tm values for the l ‐ and d ‐amino acid substitutions [(ΔTm′ = TmL and TmD)] ranging from 1°C to 34.5°C. HPLC retention times [ΔtR(XL?XD)] also had values ranging from ?0.52 to 7.31 min at pH 7.0. The helix‐destabilizing ability of a specific d ‐amino acid is highly dependent on its side‐chain, with no clear relationship to the helical propensity of its corresponding l ‐enantiomers. In both CD and reversed‐phase HPLC studies, d ‐amino acids with β‐branched side‐chains destabilize α‐helical structure to the greatest extent. A series of helix stability coefficients was subsequently determined, which should prove valuable both for protein structure‐activity studies and de novo design of novel biologically active peptides.  相似文献   

13.
Abstract: Using different stereoselective chemical and chemoenzymatic approaches we synthesized the chiral, Cα‐methylated α‐amino acid l ‐(αMe)Nva with a short, linear side‐chain. A set of terminally protected model peptides to the pentamer level containing either (αMe)Nva or Nva in combination with Ala and/or Aib was prepared using solution methods and characterized fully. Two (αMe)Nva peptides were also synthesized using side‐chain hydrogenation of the corresponding Cα‐methyl, Cα‐allylglycine (Mag) peptides. A detailed solution and crystal‐state conformational analysis based on FT‐IR absorption, 1H NMR and X‐ray diffraction techniques allowed us to define that: (i) (αMe)Nva is an effective β‐turn and 310‐helix former; and (ii) the relationship between (αMe)Nva chirality and the screw sense of the turn/helix formed is that typical of protein amino acids, i.e. l ‐(αMe)Nva induces the preferential formation of right‐handed folded structures. In more general terms, this study reinforced previous conclusions that peptides based on α‐amino acids with a Cα‐methyl substituent and a Cα‐linear alkyl substituent are characterized by a strong tendency to fold into turn and helical structures.  相似文献   

14.
Endoplasmic reticulum (ER) stress‐induced pancreatic β‐cell dysfunction and death play important roles in the development of diabetes. The 1,2,3‐triazole derivative 1 is one of only a few structures that have thus far been identified that protect β cells against ER stress. However, this compound has narrow activity range and limited aqueous solubility. To overcome these, we designed and synthesized a new scaffold in which the triazole pharmacophore was substituted with a glycine‐like amino acid. Structure–activity relationship studies on this scaffold identified a N‐(2‐(Benzylamino)‐2‐oxoethyl)benzamide analog WO5m that possesses β‐cell protective activity against ER stress with much improved potency (maximal activity at 100% with EC50 at 0.1 ± 0.01 µm ) and water solubility. Identification of this novel β‐cell protective scaffold thus provides a new promising modality for the treatment of diabetes.  相似文献   

15.
Abstract: The structural perturbation induced by CαH→Nα exchange in azaamino acid‐containing peptides was predicted by ab initio calculation of the 6‐31G* and 3‐21G* levels. The global energy‐minimum conformations for model compounds, For‐azaXaa‐NH2 (Xaa = Gly, Ala, Leu) appeared to be the β‐turn motif with a dihedral angle of φ = ± 90°, ψ = 0°. This suggests that incorporation of the azaXaa residue into the i + 2 position of designed peptides could stabilize the β‐turn structure. The model azaLeu‐containing peptide, Boc‐Phe‐azaLeu‐Ala‐OMe, which is predicted to adopt a β‐turn conformation was designed and synthesized in order to experimentally elucidate the role of the azaamino acid residue. Its structural preference in organic solvents was investigated using 1H NMR, molecular modelling and IR spectroscopy. The temperature coefficients of amide protons, the characteristic NOE patterns, the restrained molecular dynamics simulation and IR spectroscopy defined the dihedral angles [ (φi+1, ψi+1) (φi+2, ψi+2)] of the Phe‐azaLeu fragment in the model peptide, Boc‐Phe‐azaLeu‐Ala‐OMe, as [(?59°, 127°) (107°, ?4°)]. This solution conformation supports a βII‐turn structural preference in azaLeu‐containing peptides as predicted by the quantum chemical calculation. Therefore, intercalation of the azaamino acid residue into the i + 2 position in synthetic peptides is expected to provide a stable β‐turn formation, and this could be utilized in the design of new peptidomimetics adopting a β‐turn scaffold.  相似文献   

16.
Abstract: Kinetic aspects of the sensitized photooxidation of α‐ and β‐chymotrypsins have been studied at pH 6 and 8. The sensitization, employing classical O2(1Δg)‐photogenerators, such as xanthene dyes, is a kinetically intricate process because of the presence of ground state dye–protein associations and to the simultaneous participation of superoxide ion and singlet molecular oxygen [O2(1Δg)]. Both proteins, that possess the same distribution pattern of photooxidizable amino acids, suffer a pure O2(1Δg)‐mediated photodynamic attack, using the carbonylic sensitizer Perinaphthenone. Overall and reactive rate constants for the O2(1Δg)‐quenching (in the order of 108 and 107/M/s, respectively), and rates of oxygen consumption determined by time‐resolved, spectroscopic and polarographic methods indicate that α‐ and β‐chymotrypsins are less photooxidizable at pH 6, as a result of an enhancement of the O2(1Δg)‐physical quenching component. In general terms, β‐chymotrypsin exhibits the greater overall proclivity to interact with O2(1Δg), whereas structural factors, possibly evidenced by a higher exposure of the reactive tryptophan residues, impart an increased photooxidation degree to the proteins at pH 8, specially to the α‐chymotrypsin.  相似文献   

17.
Abstract: Two complete series of N‐protected oligopeptide esters to the pentamer level from 1‐amino‐cyclodecane‐1‐carboxylic acid (Ac10c), an α‐amino acid conformationally constrained through a medium‐ring Cαi ? Cαi cyclization, and either the l ‐Ala or Aib residue, along with the N‐protected Ac10c monomer and homo‐dimer alkylamides, were synthesized using solution methods and fully characterized. The preferred conformation of these model peptides was assessed in deuterochloroform solution using FT‐IR absorption and 1H NMR techniques. Furthermore, the molecular structures of two derivatives (Z‐Ac10c‐OH and Fmoc‐Ac10c‐OH) and two peptides (the dipeptide ester Z‐Ac10c‐l ‐Phe‐OMe and the tripeptide ester Z‐Aib‐Ac10c‐Aib‐OtBu) were determined in the crystal state using X‐ray diffraction. The experimental results support the view that β‐bends and 310‐helices are preferentially adopted by peptides rich in Ac10c, the third largest cycloaliphatic Cα,α‐disubstituted glycine known. This investigation allowed us to complete a detailed conformational analysis of the whole 1‐amino‐cycloalkane‐1‐carboxylic acid (Acnc, with n = 3–12) series, which represents the prerequisite for our recent proposal of the ‘Acnc scan’ concept.  相似文献   

18.
The amino acid sequence of human plasma α1-acid glycoprotein, upon comparison with the sequences of other blood proteins, was shown to possess significant similarity with the immunoglobulins. Employing direct and corrected sequence identity, the average mutation value and two different computer comparisons for the evaluation of sequence similarity, the following two regions of this α-globulin, which account for approximately half of the total amino acid sequence of the protein, were found to possess sequence similarity with the immunoglobulins. a) The region from residues 77 through 125 proved to be related to the variable region of several human H and L chains, and b) the region from residues 136 through 166 was found to be related not only to the constant region of a human and a mouse L chain but also to the third and fourth constant region of a rabbit and a human H chain, respectively. These results suggest that α1-acid glycoprotein is probably related to the immunoglobulins and further suggest that it possibly diverged from the immunoglobulin evolutionary tree prior to the formation of the primitive L chain.  相似文献   

19.
The effect of changing 1st and 4th amino acid residues on β-turn preference of tetrapeptide sequences was studied by use of CD spectra of the chromophoric derivatives, which have Dnp- and pNA-groups as the amino and carboxyl substituents, respectively. The effect was examined with the tetrapeptides having such sequences at the 2nd and 3rd positions as -L-Pro-L-Asn-, -L-Pro-Gly-, -L-Pro-D-Ala-, -L-Ala-D-Leu-, -L-Ala-L-Pro-, and -D-Ala-L-Pro-. The β-turn preferences estimated from the CD intensities of the bands due to exciton interaction were found to depend largely on the configurations of the 1st and 4th amino acid residues. When 1st and 2nd (or 3rd and 4th) residues had the same configuration, decreased intensity of the CD band was observed even if the internal sequence had high β-turn preference. Terminal Gly residues were favorable for the β-turn conformation in many of the tetrapeptide sequences examined.  相似文献   

20.
In this study, we propose a novel molecular platform‐integrated fluorinated antitumor nitrogen mustards for 19F‐MRS assay of β‐galactosidase (β‐gal) activity. Following this idea, we have designed, synthesized, and characterized 2‐fluoro‐4‐[bis(2′‐chloroethyl)amino]phenyl β‐D‐galactopyranoside 5 , 2‐fluoro‐4‐{bis[2′‐O‐(β‐D‐galactopyranosyl)ethyl]amino}phenyl β‐D‐galactopyranoside 8 , 2‐fluoro‐4‐{bis[[1″‐(β‐D‐galactopyranosyl)‐1″, 2″, 3″‐triazol‐4″‐yl]methyl] amino}phenyl β‐D‐galactopyranoside 14 and 2‐fluoro‐4‐{bis[[1″‐(β‐D‐glucopyranosyl)‐1″, 2″, 3″‐triazol‐4″‐yl]methyl]amino}phenyl β‐D‐galactopyranoside 15 through glycosylation and click reaction strategies, and their structures were confirmed by NMR and HRMS or elemental analysis data. Among them, 2‐fluoro‐4‐[bis(2′‐chloroethyl)amino]phenyl β‐D‐galacto‐pyranoside 5 was found very sensitive to β‐gal (E801A) in PBS at 37°C with big ΔδF response. Here, we demonstrated the feasibility of this platform for assessing β‐gal activity in solution, and in vitro with lacZ‐transfected human MCF7 breast and PC3 prostate tumor cells, by the characterization of β‐gal‐responsive 19F‐chemical shift changes ΔδF and hydrolytic kinetics.  相似文献   

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