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1.
Possible combinations of βαβ-units and Π-like modules in proteins in both right- and left-handed forms have been analyzed in detail. The correlation between the mutual arrangement of the structural elements in the polypeptide chain and their handedness has been shown. In the βαβΠ combinations, which is encountered most frequently in proteins, the Π-module follows the βαβ unit along the chain and both elements are right-handed. In the Πβαβ combinations, where the Π-module is located at the N end and the βαβ-unit follows it, the former is left-handed and the latter is right-handed. In relatively rare combinations of the left-handed βαβ-units and right-handed Π-modules, the βαβ-unit follows Π-module in the chain. The combinations of left-handed Π-modules and the left-handed βαβ-units are unobservable in proteins. It has also been shown that the Π-modules with a β-strand—α-helix—arch—β-strand structure are observed in proteins only in a right-handed form and half of them (51%) contains cis-prolines in their arches. These arches of nonhomologous proteins, as well as the positions of cis-prolines, nearly coincide when superimposed. The superimposed Π-modules also demonstrate that their overall folds are very similar. Structural alignment of their amino acid sequences has shown that the Π-modules have very similar sequence patterns of the key hydrophobic, hydrophilic, glycine, and cis-proline residues. 相似文献
2.
3.
Y. S. Shouche P. K. Latha N. Ramesh K. Majumder V. Mandyan Samir K. Brahmachari 《Journal of biosciences》1985,8(3-4):563-578
We have investigated structural transitions in Poly(dG-dC) and Poly(dG-Me5dC) in order to understand the exact role of cations in stabilizing left-handed helical structures in specific sequences andthe
biological role, if any, of these structures. From a novel temperature dependent Z ⇌ B transition it has been shown that a
minor fluctuation in Na+ concentration at ambient temperature can bring about B to Z transition. Forthe first time, wehave observed a novel Z⇌B⇌Zuble
transition in poly(dG-Me5dC) as the Na+ concentration is gradually increased. This suggests that a minor fluctuation in Na+ concentration in conjunction with methylation may transform small stretches of CG sequences from one conformational state
to another. These stretches could probably serve as sites for regulation. Supercoiled formV DNA reconstituted from pBR322
and pβG plasmids have been studied as model systems, in order to understand the nature and role of left-handed helical conformation
in natural sequences. A large portion of DNA in form V, obtained by reannealing the two complementary singlestranded circles
is forced to adopt left-handed double helical structure due to topological constraints (L
k = 0). Binding studies with Z-DNA specific antibody and spectroscopic studies confirm the presence of left-handed Z-structure
in the pβG and pβR322 form V DNA. Cobalt hexamine chloride, which induces Z-form in Poly(dG-dC) stabilizes the Z-conformation
in form V DNA even in the non-alternating purine-pyrimidine sequences. A reverse effect is observed with ethidium bromide.
Interestingly, both topoisomerase I and II (from wheat germ) act effectively on form V DNA to give rise to a species having
an electrophoretic mobility on agarose gel similar to that of open circular (form II) DNA. Whether this molecule is formed
as a result of the left-handed helical segments of form V DNA undergoing a transition to the right-handed B-form during the
topoisomerase action remains to be solved. 相似文献
4.
Using yeast two-hybrid system to detect interactions of ATP synthase subunits from Spinacia oleracea
Subunit interactions among the chloroplast ATP synthase subunits were studied using the yeast two-hybrid system. Various pairwise
combinations of genes encoding α, β, γ, δ and ε subunits ofSpinach ATP synthase fused to the binding domain or activation domain of GAL4 DNA were introduced into yeast and then expression
of a reporter gene encoding β-galactosidase was detected. Of all the combinations, that of γ and ε subunit genes showed the
highest level of reporter gene expression, while those of α and β, a and ε, β and ε and β and δ induced stable and significant
reporter gene expression. The combination of δ and ε as well as that of δ and γ induced weak and unstable reporter gene expression.
However, combinations of α and γ, β and γ and α and δ did not induce reporter gene expression. These results suggested that
specific and strong interactions between γ and ε, α and β, α and ε, β and ε and β and δ subunits, and weak and transient interactions
between δ and ε and δ and γ subunits occurred in the yeast cell in the two-hybrid system. These results give a new look into
the structural change of ATP synthase during catalysis. 相似文献
5.
Subunit interactions among the chloroplast ATP synthase subunits were studied using the yeast two-hybrid system. Various pairwise
combinations of genes encoding α, β, γ, δ and ε subunits ofSpinach ATP synthase fused to the binding domain or activation domain of GAL4 DNA were introduced into yeast and then expression
of a reporter gene encoding β-galactosidase was detected. Of all the combinations, that of γ and ε subunit genes showed the
highest level of reporter gene expression, while those of α and β, a and ε, β and ε and β and δ induced stable and significant
reporter gene expression. The combination of δ and ε as well as that of δ and γ induced weak and unstable reporter gene expression.
However, combinations of α and γ, β and γ and α and δ did not induce reporter gene expression. These results suggested that
specific and strong interactions between γ and ε, α and β, α and ε, β and ε and β and δ subunits, and weak and transient interactions
between δ and ε and δ and γ subunits occurred in the yeast cell in the two-hybrid system. These results give a new look into
the structural change of ATP synthase during catalysis. 相似文献
6.
Giampiero De Sanctis Anna Maria Priori Francesca Polizio Paolo Ascenzi M. Coletta 《Journal of biological inorganic chemistry》1998,3(2):135-139
The X-band EPR spectroscopic features of the ferrous nitrosylated derivative of α(Fe)2β(Co)2 and of α(Co)2β(Fe)2 metal hybrids of human hemoglobin (Hb) have been investigated at pH 7.0 and analyzed in parallel with those of the native
nitrosylated tetramer (HbNO). The effect of 2,3-biphosphoglycerate (BPG), inositol hexakisphosphate (IHP) and bezafibrate
(BZF) has been investigated in order to understand the perturbations induced on α and β subunits in the tetramer by the binding
of allosteric effectors. A large perturbation is observed in both subunits upon BZF binding, while in the case of IHP only
α-chains are affected; on the other hand, BPG leaves both chains essentially unperturbed. Thus, different binding modes of
allosteric effectors to HbNO may occur, and the simultaneous addition of two effector molecules, namely BPG and BZF or IHP
and BZF to HbNO, brings about different alterations of the X-band EPR spectroscopic properties. This behavior indicates that
the intramolecular communication pathway(s) between the heme and the binding pockets of the heterotropic ligands (i.e., IHP
and BZF, or BPG and BZF) are different, leading to distinct structural perturbations.
Received: 19 September 1997 / Accepted: 16 December 1997 相似文献
7.
Summary. The support vector machine, a machine-learning method, is used to predict the four structural classes, i.e. mainly α, mainly
β, α–β and fss, from the topology-level of CATH protein structure database. For the binary classification, any two structural
classes which do not share any secondary structure such as α and β elements could be classified with as high as 90% accuracy.
The accuracy, however, will decrease to less than 70% if the structural classes to be classified contain structure elements
in common. Our study also shows that the dimensions of feature space 202 = 400 (for dipeptide) and 203 = 8 000 (for tripeptide) give nearly the same prediction accuracy. Among these 4 structural classes, multi-class classification
gives an overall accuracy of about 52%, indicating that the multi-class classification technique in support of vector machines
may still need to be further improved in future investigation. 相似文献
8.
Leitgeb B Kerényi A Bogár F Paragi G Penke B Rákhely G 《Journal of molecular modeling》2007,13(11):1141-1150
Poly-(Ala) and poly-(Gln) peptides have important biological effects, and can cause various human illnesses and neurodegenerative
diseases. Conformational analysis of these homo-oligopeptides (HOPs) was carried out by simulated annealing in order to identify
their structural properties regarding secondary structures and intramolecular H-bonding patterns. Poly-(Ala) and poly-(Gln)
peptides composed of 7, 10, 14 or 20 amino acids were modelled in both charged and terminally blocked forms. In the case of
conformers derived from simulated annealing calculations, the presence of various secondary structural elements (different
types of β-turns, α-helix, 310-helix, poly-proline II helix, parallel and antiparallel β-strands) was investigated. Moreover, the intramolecular H-bonding
patterns formed either between the backbone atoms for both HOPs or between the backbone and side-chain atoms for the poly-(Gln)
peptides were examined. Our results showed that different secondary structural elements (type I and type III β-turns, α-helix,
310-helix, antiparallel β-strand) could be observed in both poly-(Ala) and poly-(Gln) peptides and, according to their presence,
characteristic H-bonding patterns formed mainly by i←i+3 and i←i+4 H-bonds could be found. 相似文献
9.
The Na,K-ATPase is a major ion transport protein found in higher eukaryotic cells. The enzyme is composed of two subunits,
α and β, and tissue-specific isoforms exist for each of these, α1, α2 and α3 and β1, β2 and β3. We have proposed that an additional
α isoform, α4, exists based on genomic and cDNA cloning. The mRNA for this gene is expressed in rats and humans, exclusively
in the testis, however the expression of a corresponding protein has not been demonstrated. In the current study, the putative
α4 isoform has been functionally characterized as a novel isoform of the Na,K-ATPase in both rat testis and in α4 isoform
cDNA transfected 3T3 cells. Using an α4 isoform-specific polyclonal antibody, the protein for this novel isoform is detected
for the first time in both rat testis and in transfected cell lines. Ouabain binding competition assays reveal the presence
of high affinity ouabain receptors in both rat testis and in transfected cell lines that have identical K
D
values. Further studies of this high affinity ouabain receptor show that it also has high affinities for both Na+ and K+. The results from these experiments definitively demonstrate the presence of a novel isoform of the Na,K-ATPase in testis.
Received: 4 December 1998/Revised: 1 February 1999 相似文献
10.
In the present study, pathways of growth of protein structures represented in the structural tree for β-proteins containing
3β-corners are analyzed. It is shown that the frequency of occurrence of the completed structures of known proteins within
branches of the tree is quite different. This means that allowed pathways of growth of protein structures are not equal and
their usage is quite different. In most cases, addition of one or two β-strands nearest along the chain to the root 3β-corner
(67%) or addition of three β-strands to the 3β-corner results in the formation of structures closed into cycles or barrels.
Therefore, the pathways that result in closed structures are used most often in the first steps of growth of the root 3β-corner.
Amino acid sequences coding for left-handed superhelices that close into cycles the 3β-corners are also analyzed. It is demonstrated
that most crossover sites where the polypeptide chain passes from one β-layer to the other have one or two residues in sterically
constrained αL- or ɛ-conformations, which should be glycines or residues with flexible side chains in order to reduce the steric constraints. 相似文献
11.
Aimed at understanding the crucially important structural features for the integrity of α-helical mimicry by βγ-sequences,
an α-amino acid sequence in a native peptide was substituted by differently arranged βγ-sequences. The self- and hetero-assembly
of a series of αβγ-chimeric sequences based on a 33-residue GCN4-derived peptide was investigated by means of molecular dynamics,
circular dichroism, and a disulfide exchange assay. Despite the native-like behavior of βγ alternating sequences such as retention
of α-helix dipole and the formation of 13-membered α-helix turns, the αβγ-chimeras with different βγ substitution patterns
do not equally mimic the structural behavior of the native parent peptide in solution. The preservation of the key residue
contacts such as van der Waals interactions and intrahelical H-bonding, which can be met only by particular substitution patterns,
thermodynamically favor the adoption of coiled coil folding motif. In this study, we show how successfully the destabilizing
structural consequences of α → βγ modification can be harnessed by reducing the solvent-exposed hydrophobic surface area and
placing of suitably long and bulky helix-forming side chains at the hydrophobic core. The pairing of αβγ-chimeric sequences
with the native wild-type are thermodynamically allowed in the case of ideal arrangement of β- and γ-residues. This indicates
a similarity in local side chain packing of β- and γ-amino acids at the helical interface of αβγ-chimeras and the native α-peptide.
Consequently, the backbone extended residues are able to participate in classical “knob-into-hole” packing with native α-peptide. 相似文献
12.
Carlos P. Alvarado-Díaz Julio C. Tapia Marcelo Antonelli Ricardo D. Moreno 《Cell and tissue research》2009,338(1):139-149
Protein kinase CK2 is a serine/threonine kinase expressed in organisms from yeast to human and is composed of a catalytic
subunit (α or α’) and a regulatory subunit (β) forming a holoenzyme with the possible subunit combinations α2β2, α’2β2, or αα’β2. This kinase has been shown to be involved in embryonic development and gametogenesis. We have studied the expression of
the CK2α’ and CK2β subunits during the first wave of spermatogenesis and in adult testis in the rat. Western blot analyses
have demonstrated that both CK2α’ and CK2β are expressed in testes from birth to adulthood. A more detailed study of the protein
localization of CK2α’ and CK2β by immunohistochemistry suggests that CK2α’ and CK2β are localized in the nuclei of Sertoli
cells in 5-day-old rats, whereas they appear to have a cytoplasmic localization in older animals. In adult testes, CK2α’ and
CK2β subunits are present in spermatocytes. Both subunits exhibit a similar expression pattern with the highest level in spermatocytes
at stages VIII-XIV. Interestingly, CK2β is highly expressed in spermatogonia, whereas CK2α’ is barely detectable. Mature epididymal
spermatozoa express CK2α’ in the acrosome and CK2β in the flagellum. This new evidence therefore indicates that protein kinase
CK2 has a possible role at various stages during mammalian spermatogenesis, a process that involves proliferation, meiosis,
apoptosis, and differentiation. CK2 might thus emerge as a new pivotal control enzyme at various levels in mammalian spermatogenesis. 相似文献
13.
Eric Mossel Fernando Formaggio Giovanni Valle Marco Crisma Claudio Toniolo Mitsunobu Doi Toshimasa Ishida Quirinus B. Broxterman Johan Kamphuis 《International journal of peptide research and therapeutics》1998,5(2-3):223-225
Summary In order to obtain further information on the role played by phenyl ring position in the Cα-methylated α-amino acid side chain on peptide preferred conformation, the crystal-state structural preferences of Cα-methyl, Cα-phenylglycine peptides have been determined by X-ray diffraction. This study shows that either the fully extended conformation
or the β-bend/310-helical structures are adopted by peptides characterized by this Cα-methylated, β-branched, aromatic α-amino acid. 相似文献
14.
Benedetti Ettore Iacovino Rosa Pedone Carlo Rossi Filomena Saviano Michele Isernia Carla Montesarchio Daniela de Napoli Lorenzo Piccialli Gennaro 《International journal of peptide research and therapeutics》1997,4(3):129-134
Summary An N- and C-protected derivative ofhomo-β-leucine, Fmoc-homo-β-(S)-leucine methyl ester, synthesized from the corresponding proteinogenic parent α-amino acid in enantiopure form has been
fully characterized in the solid state by X-ray diffraction analysis. The crystal conformation of this new residue indicates
and extended conformation for thishomo-β-residue, with the ϕ torsion angle being more constrained than the μ and ψ angles. 相似文献
15.
Lactobacillus casei CRL705 produces a class IIb bacteriocin, lactocin 705, which relies on the complementary action of two components, Lac705α
and Lac705β. These peptides exert a bactericidal effect on the indicator strain Lactobacillus plantarum CRL691, with an optimal Lac705α/Lac705β peptide ratio of 1 to 4. Electron microscopy studies showed that treated CRL691 cells
have their cell wall severely damaged, with mesosome-like membranous formations protruding into their cytoplasm. Although
less pronounced, a similar effect was also observed with the Lac705β peptide alone. Furthermore, Lac705β increased the inhibitory
action of a diluted supernatant of L. casei CRL705, while Lac705α protected CRL691 cells from inhibition. Both peptides were required to dissipate the proton motive
force (Δψ and ΔpH) of CRL691 cells. These data suggested that of the two components of lactocin 705, the Lac705α peptide is
responsible for receptor recognition, and the Lac705β peptide is the active component on the cell membrane of CRL691 cells.
Received: 12 April 2002 / Accepted: 24 May 2002 相似文献
16.
N. G. Esipova L. E. Ragulina L. I. Davydova V. M. Lobachev V. Yu. Makeev V. G. Bogush V. G. Tumanyan V. G. Debabov 《Biophysics》2009,54(3):271-274
The distribution of secondary structure elements along the polypeptide chains of spider silk proteins spidroins 1 and 2 and
their recombinant analogs has been studied by statistical methods. It was found that these proteins as monomers contain only
traces of β-structure, while the Ala-rich and the Gly-rich regions are predicted as α-helices and as left-handed helices of
polyproline II type. Analysis of literature and our CD data shows that the major polypeptide chain conformation of spidroins
1 and 2 and their recombinant analogs in aqueous solutions is the polyproline II helix, with some α-helices and a very small
share of β-structures. The transition to the state with extended conformations, which are characteristic of mature silk fibers,
requires dehydration of the polypeptide backbone. Thus, the genesis of β-structure in spider web proteins is determined by
the conditions of transitions between the main regular backbone conformations. 相似文献
17.
V. G. Tumanyan Yu. A. Neyfack M. K. Pirtskhalava J. H. Männik 《Journal of biosciences》1985,8(3-4):593-602
On the basis of complete scanning through conformational space of dihedral angles, twelve structural genera were obtained.
Subsequent energy minimization within these genera yielded a limited set of duplexes with stacking: right-handed B-form (Wilkins
type), B2-form (Watson and Crick type) and left-handed Ll-form (Sasisekharan type) and the new L2-form. In the polymeric DNA
only right-handed double-helices are possible, the left-handed helices are forbidden due to poor 1–5 interchain contacts.
In contrast, for short fragments the left- and right-handed helicek have practically the same energies providing some physical
ground for side-by-side form, which biologically is possible as recombination form and may be as replication form. 相似文献
18.
The β-subunit of high-voltage-activated (HVA) calcium channels is essential for the regulation of expression and gating. On
the other hand, various reports have suggested that β subunits play no role in the regulation of low-voltage-activated T-type
channels. In addition there has been no clear demonstration of a physical interaction between the α-subunit of T-type channel
with β-subunit. In this study, we systematically investigated the interaction between CaVα and CaVβ. The four CaVβ isoforms were expressed in a bacterial system and purified into homogeneity, whereas the ten types of CaVα alpha interaction domain (AID) peptides were chemically synthesized. All possible combinations of CaVα and CaVβ were then tested for by in vitro immunoassays. We describe here the identification of a new interaction between CaV3.3 and CaVβ proteins. This interaction is of low affinity compared to that between the AID of the HVA α-subunit and the alpha-binding
pocket (ABP) site of the β-subunit. The AID peptide of HVA channel exerted no effect on the CaV3.3-CaVβ interaction, thus demonstrating that another site not in the ABP of CaVβ protein played a role in binding with CaV3.3. This is the first demonstration of an α-β subunit interaction in a T-type calcium channel. 相似文献
19.
Nie H Li Z Lukas RJ Shen Y Song L Wang X Yin M 《Cellular and molecular neurobiology》2008,28(1):103-112
(1) Nicotinic acetylcholine receptors in central nervous system are thought to be new targets for Alzheimer’s disease. However,
the most involved nicotinic receptor subtype in Alzheimer’s disease is unclear. α4β2 receptor is the most widely spread subtype
in brain, involving in several important aspects of cognitive and other functions. We constructed cell line by transfecting
human amyloid precursor protein (695) gene into SH-EP1 cells which have been transfected with human nicotinic receptor α4
subunit and β2 subunit gene, to observe effects of α4β2 receptors activation on β-amyloid, expecting to provide a new cell
line for drug screening and research purpose. (2) Liposome transfection was used to express human amyloid precursor protein
(695) gene in SH-EP1-α4β2 cells. Function of the transfected α4β2 receptors was tested by patch clamp. Effects of nicotine
and epibatidine (selective α4β2 nicotinic receptor agonist) on β-amyloid were detected by Western blot and ELISA. Effects
of nicotine and epibatidine on amyloid precursor protein (695) mRNA level were measured using real-time PCR. (3) Human amyloid
precursor protein (695) gene was stably expressed in SH-EP1-α4β2 cells; Nicotine (1 μM) and epibatidine (0.1 μM) decreased
intracellular and secreted β-amyloid in the cells; and activation of α4β2 receptors did not affect amyloid precursor protein
(695) mRNA level. (4) These results suggest that the constructed cell line, expressing both amyloid precursor protein (695)
gene and human nicotinic receptor α4 subunit and β2 subunit gene, might be useful for screening specific nicotinic receptor
agonists against Alzheimer’s disease. Alteration of Aβ level induced by activation of α4β2 nAChR in our study might occur
at a post-translational level. 相似文献
20.
Rameshwaram NR Karanam NK Scharf C Völker U Nadimpalli SK 《Glycoconjugate journal》2009,26(2):161-172
A new unique lectin (galactose-specific) purified from the seeds of Dolichos lablab, designated as DLL-II is a heterodimer composed of closely related subunits α and β. These were separated by SDS-PAGE and
isolated by electroelution. By ESI-MS analysis their molecular masses were found to be 30.746 kDa (α) and 28.815 kDa (β) respectively.
Both subunits were glycosylated and displayed similar amino acid composition. Using advanced mass spectrometry in combination
with de novo sequencing and database searches for the peptides derived by enzymatic and chemical cleavage of these subunits, the primary
sequence was deduced. This revealed DLL-II to be made of two polypeptide chains of 281(α) and 263(β) amino acids respectively.
The β subunit differed from the α subunit by the absence of some amino acids at the carboxy terminal end. This structural
difference suggests that possibly, the β subunit is derived from the α subunit by posttranslational proteolytic modification
at the COOH-terminus. Comparison of the DLL-II sequence to other leguminous seed lectins indicates a high degree of structural
conservation.
Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献