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1.
Background
For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue γ-turn to six-residue π-turn. The Schellman motif occurring at the C-terminal end of α-helices is a classical example of hydrogen bonded π-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded β- and α-turns have been identified previously; likewise, a systematic characterization of π-turns would provide valuable insight into turn structures. 相似文献2.
Background
β-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains. 相似文献3.
The secondary structure of the trimeric protein 4-chlorobenzoyl coenzyme A dehalogenase from Arthrobacter sp. strain TM-1, the second of three enzymes involved in the dechlorination of 4-chlorobenzoate to form 4-hydroxybenzoate, has
been examined. EmM for the enzyme was 12.59. Analysis by circular dichroism spectrometry in the far uv indicated that 4-chlorobenzoyl coenzyme
A dehalogenase was composed mostly of α-helix (56%) with lesser amounts of random coil (21%), β-turn (13%) and β-sheet (9%).
These data are in close agreement with a computational prediction of secondary structure from the primary amino acid sequence,
which indicated 55.8% α-helix, 33.7% random coil and 10.5% β-sheet; the enzyme is, therefore, similar to the 4-chlorobenzoyl
coenzyme A dehalogenase from Pseudomonas sp. CBS-3. The three-dimensional structure, including that of the presumed active site, predicted by computational analysis,
is also closely similar to that of the Pseudomonas dehalogenase. Study of the stability and physicochemical properties revealed that at room temperature, the enzyme was stable
for 24 h but was completely inactivated by heating to 60°C for 5 min; thereafter by cooling at 1°C min−1 to 45°C, 20.6% of the activity could be recovered. Mildly acidic (pH 5.2) or alkaline (pH 10.1) conditions caused complete
inactivation, but activity was fully recovered on returning the enzyme to pH 7.4. Circular dichroism studies also indicated
that secondary structure was little altered by heating to 60°C, or by changing the pH from 7.4 to 6.0 or 9.2. Complete, irreversible
destruction of, and maximal decrease in the fluorescence yield of the protein at 330–350 nm were brought about by 4.5 M urea
or 1.1 M guanidinium chloride. Evidence was obtained to support the hypothetical three-dimensional model, that residues W140
and W167 are buried in a non-polar environment, whereas W182 appears at or close to the surface of the protein. At least one
of the enzymes of the dehalogenase system (the combined 4-chlorobenzoate:CoA ligase, the dehalogenase and 4-hydroxybenzoyl
coenzyme A thioesterase) appears to be capable of association with the cell membrane.
相似文献
Anthony R. W. SmithEmail: |
4.
Background
Protein tertiary structure can be partly characterized via each amino acid's contact number measuring how residues are spatially arranged. The contact number of a residue in a folded protein is a measure of its exposure to the local environment, and is defined as the number of C β atoms in other residues within a sphere around the C β atom of the residue of interest. Contact number is partly conserved between protein folds and thus is useful for protein fold and structure prediction. In turn, each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis from sequence data. In this study, we provide a more accurate contact number prediction method from protein primary sequence. 相似文献5.
Rudresh Acharya Madhvi Gupta Suryanarayanarao Ramakumar Udupi A Ramagopal Virander S Chauhan 《BMC structural biology》2007,7(1):51
Background
The de novo design of peptides and proteins has recently surfaced as an approach for investigating protein structure and function. This approach vitally tests our knowledge of protein folding and function, while also laying the groundwork for the fabrication of proteins with properties not precedented in nature. The success of these studies relies heavily on the ability to design relatively short peptides that can espouse stable secondary structures. To this end, substitution with α, β-dehydroamino acids, especially α, β-dehydrophenylalanine (ΔPhe) comes in use for spawning well-defined structural motifs. Introduction of ΔPhe induces β-bends in small and 310-helices in longer peptide sequences. 相似文献6.
Numerous methods for predicting γ-turns in proteins have been developed. However, the results they generally provided are
not very good, with a Matthews correlation coefficient (MCC) ≤0.18. Here, an attempt has been made to develop a method to
improve the accuracy of γ-turn prediction. First, we employ the geometric mean metric as optimal criterion to evaluate the
performance of support vector machine for the highly imbalanced γ-turn dataset. This metric tries to maximize both the sensitivity
and the specificity while keeping them balanced. Second, a predictor to generate protein shape string by structure alignment
against the protein structure database has been designed and the predicted shape string is introduced as new variable for
γ-turn prediction. Based on this perception, we have developed a new method for γ-turn prediction. After training and testing
the benchmark dataset of 320 non-homologous protein chains using a fivefold cross-validation technique, the present method
achieves excellent performance. The overall prediction accuracy Q
total can achieve 92.2% and the MCC is 0.38, which outperform the existing γ-turn prediction methods. Our results indicate that
the protein shape string is useful for predicting protein tight turns and it is reasonable to use the dihedral angle information
as a variable for machine learning to predict protein folding. The dataset used in this work and the software to generate
predicted shape string from structure database can be obtained from anonymous ftp site freely. 相似文献
7.
8.
Background
Capping protein (CP), a heterodimer of α and β subunits, is found in all eukaryotes. CP binds to the barbed ends of actin filaments in vitro and controls actin assembly and cell motility in vivo. Vertebrates have three isoforms of CPβ produced by alternatively splicing from one gene; lower organisms have one gene and one isoform. 相似文献9.
The PsbH protein of cyanobacterium Synechocystis sp. PCC 6803 was expressed as a fusion protein with glutathione-S transferase (GST) in E. coli grown on a mineral medium enriched in 15N isotope. After enzymatic cleavage of the fusion protein, the 1H-15N-HSQC spectrum of PsbH protein in presence of the detergent β-D-octyl-glucopyranoside (OG) was recorded on a Bruker DRX 500 MHz NMR spectrometer equipped with a 5 mm TXI cryoprobe to enhance the sensitivity and resolution. Non-labelled protein
was used for secondary structure estimation by deconvolution from circular dichroism (CD) spectra. Experimental results were
compared with our results from a structural model of PsbH using a restraint-based comparative modelling approach combined
with molecular dynamics and energetic modelling. We found that PsbH shows 34–38% α-helical structure (Thr36-Ser60), a maximum
of around 15% of β-sheet, and 12–19% of β-turn. 相似文献
10.
Background
Protein O-GlcNAcylation (or O-GlcNAc-ylation) is an O-linked glycosylation involving the transfer of β-N-acetylglucosamine to the hydroxyl group of serine or threonine residues of proteins. Growing evidences suggest that protein O-GlcNAcylation is common and is analogous to phosphorylation in modulating broad ranges of biological processes. However, compared to phosphorylation, the amount of protein O-GlcNAcylation data is relatively limited and its annotation in databases is scarce. Furthermore, a bioinformatics resource for O-GlcNAcylation is lacking, and an O-GlcNAcylation site prediction tool is much needed. 相似文献11.
Verena Kriechbaumer Linda Weigang Andreas Fießelmann Thomas Letzel Monika Frey Alfons Gierl Erich Glawischnig 《BMC plant biology》2008,8(1):44
Background
In bacteria, such as Salmonella typhimurium, tryptophan is synthesized from indole-3-glycerole phosphate (IGP) by a tryptophan synthase αββα heterotetramer. Plants have evolved multiple α (TSA) and β (TSB) homologs, which have probably diverged in biological function and their ability of subunit interaction. There is some evidence for a tryptophan synthase (TS) complex in Arabidopsis. On the other hand maize (Zea mays) expresses the TSA-homologs BX1 and IGL that efficiently cleave IGP, independent of interaction with TSB. 相似文献12.
Background
The majority of residues in protein structures are involved in the formation of α-helices and β-strands. These distinctive secondary structure patterns can be used to represent a protein for visual inspection and in vector-based protein structure comparison. Success of such structural comparison methods depends crucially on the accurate identification and delineation of secondary structure elements. 相似文献13.
V. S. Ananthanarayanan S. K. Attah-poku P. L. Mukkamala P. H. Rehse 《Journal of biosciences》1985,8(1-2):209-221
We report here two sets of results on proline-containing linear peptides, one of which brings out the role of theβ-turn conformation in the structure of nascent collagen while the other points to the functional importance of the β-turn
in calcium-binding proteins. Based on the data on peptides containing the -Pro-Gly-sequence, we had proposed and experimentally
verified that theβ-turn conformation in these peptides is a structural requirement for the enzymic hydroxylation of the proline residues in
the nascent (unhydroxylated) procollagen molecule. Our recent data, presented here, on the conformation of peptides containing
both the -Pro-Gly- and -Gly-Pro-sequences reveal that while theβ-turn in the substrate molecule is required at the catalytic site of prolyl hydroxylase, the polyproline-II structure is necessary
for effective binding at the active site of the enzyme. Thus, peptides containing either theβ-turn or the polyproline-II structure alone are found to act only as inhibitors while those with the polyproline-II followed
byβ-turn serve as substrates of the enzyme. In another study, we have synthesized the two linear peptides: Boc-Pro-D-Ala-Ala-NHCH3 and Boc-Pro-Gly-Ala-NHCH3 each of which adopts, in solution, a structure with two consecutiveβ-turns, as judged from circular dichroism, infrared and nuclear magnetic resonance data. Drastic spectral changes are seen
in these peptides on binding to Ca2+. Both the peptides show a distinct specificity to Ca2+ over Mg2+, Na+ and Li+. A conformational change in the peptides occurs on Ca2+ binding which brings together the carbonyl groups to coordinate with the metal ion. These results imply a functional role
for theβ-turn in Ca2+ — binding proteins. 相似文献
14.
Background
Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures) from primary sequence data which makes use of Parallel Cascade Identification (PCI), a powerful technique from the field of nonlinear system identification. 相似文献15.
Background
We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of C α traces for short proteins (up to 200 amino acids). 相似文献16.
Background
Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. 相似文献17.
Background
The serine/threonine kinase StkP of Streptococcus pneumoniae is a major virulence factor in the mouse model of infection. StkP is a modular protein with a N-terminal kinase domain a C-terminal PASTA domain carrying the signature of penicillin-binding protein (PBP) and prokaryotic serine threonine kinase. In laboratory cultures, one target of StkP is the phosphoglucosamine mutase GlmM involved in the first steps of peptidoglycan biosynthesis. In order to further elucidate the importance of StkP in S. pneumoniae, its role in resistance to β-lactams has been assessed by mutational analysis in laboratory cultures and its genetic conservation has been investigated in isolates from infected sites (virulent), asymptomatic carriers, susceptible and non-susceptible to β-lactams. 相似文献18.
Circular dichroism spectra of proteins are extremely sensitive to secondary structure. Nevertheless, circular dichroism spectra
should not be analyzed for protein secondary structure unless they are measured to at least 184 nm. Even if all the various
types ofβ-turns are lumped together, there are at least 5 different types of secondary structure in a protein (α-helix, antiparallelβ-sheet, parallelβ-sheet,β-turn, and other structures not included in the first 4 categories). It is not possible to solve for these 5 parameters unless
there are 5 equations. Singular value decomposition can be used to show that circular dichroism spectra of proteins measured
to 200 nm contain only 2 pieces of information, while spectra measured to 190 nm contain about 4. Adding the constraint that
the sum of secondary structures must equal 1 provides another piece of information, but even with this constraint, spectra
measured to 190 nm simply do not analyze well for the 5 unknowns in secondary structure. Spectra measured to 184 nm do contain
5 pieces of information and we have used such spectra successfully to analyze a variety of proteins for their component secondary
structures. 相似文献
19.
Miryana Mircheva Diana Boy Benjamin Weiche Friederike Hucke Peter Graumann Hans-Georg Koch 《BMC biology》2009,7(1):76
Background
The signal recognition particle (SRP) receptor plays a vital role in co-translational protein targeting, because it connects the soluble SRP-ribosome-nascent chain complex (SRP-RNCs) to the membrane bound Sec translocon. The eukaryotic SRP receptor (SR) is a heterodimeric protein complex, consisting of two unrelated GTPases. The SRβ subunit is an integral membrane protein, which tethers the SRP-interacting SRα subunit permanently to the endoplasmic reticulum membrane. The prokaryotic SR lacks the SRβ subunit and consists of only the SRα homologue FtsY. Strikingly, although FtsY requires membrane contact for functionality, cell fractionation studies have localized FtsY predominantly to the cytosolic fraction of Escherichia coli. So far, the exact function of the soluble SR in E. coli is unknown, but it has been suggested that, in contrast to eukaryotes, the prokaryotic SR might bind SRP-RNCs already in the cytosol and only then initiates membrane targeting. 相似文献20.