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71.
In this paper we propose a classification of the amphipathic helical repeats occurring in the plasma apolipoprotein sequences. It is based upon the calculation of the molecular hydrophobicity potential around the helical segments. The repeats were identified using a new autocorrelation matrix, based upon similarities of hydrophobic and hydrophilic properties of the amino acid residues within the apolipoprotein sequences. The helices were constructed by molecular modeling, the molecular hydrophobicity potential was calculated, and isopotential contour lines drawn around the helices yielded a three-dimensional visualization of the hydrophobicity potential. Two classes of apolipoproteins could be differentiated by comparing the hydrophobic angles obtained by projection of the isopotential contour lines on a plane perpendicular to the long axis of the helix. The isopotential contour lines around apo AI, AIV, and E are more hydrophilic than hydrophobic, whereas they are of similar intensity for apo AII, CI, and CIII. In both cases discoidal lipid-protein complexes are generated, with the amphipathic helices around the edge of the lipid core. The long axis of the helices is oriented parallel to the phospholipid acyl chains and the hydrophilic side of the helix toward the aqueous phase. As a result of the differences in hydrophobicity potential, the contact between the hydrophobic side of the helices and the phospholipid acyl chains is larger for apo AII, CI, and CIII than for the other apolipoproteins. This might account for the greater stability of the discoidal complexes generated between phospholipids and these apoproteins. 相似文献
72.
The three-dimensional structure of the human immunoglobulin fragment Fab New (IgG1, lambda) has been refined to a crystallographic R-factor of 16.9% to 2 A resolution. Rms deviations of the final model from ideal geometry are 0.014 A for bond distances and 3.03 degrees for bond angles. Refinement was based on a new X-ray data set including 28,301 reflections with F > 2.5 sigma(F) from 6.0 to 2.0 A resolution. The starting model for the refinement procedure reported here is from the Brookhaven Protein Data Bank entry 3FAB (rev. 1981). Differences between the initial and final models include modified polypeptide-chain folding in the third complementarity-determining region (CDR3) and the third framework region (FR3) of VH and in some exposed loops of CL and CH1. Amino acid sequence changes were determined at a number of positions by inspection of difference electron density maps. The incorporation of amino acid sequence changes results in an improved VH framework model for the "humanization" of monoclonal antibodies. 相似文献
73.
J P Scheerlinck I Lasters M Claessens M De Maeyer F Pio P Delhaise S J Wodak 《Proteins》1992,12(4):299-313
A systematic survey of seven parallel alpha/beta barrel protein domains, based on exhaustive structural comparisons, reveals that a sizable proportion of the alpha beta loops in these proteins--20 out of a total of 49--belong to either one of two loop types previously described by Thornton and co-workers. Six loops are of the alpha beta 1 type, with one residue between the alpha-helix and beta-strand, and 13 are of the alpha beta 3 type, with three residues between the helix and the strand. Protein fragments embedding the identified loops, and termed alpha beta connections since they contain parts of the flanking helix and strand, have been analyzed in detail revealing that each type of connection has a distinct set of conserved structural features. The orientation of the beta-strand relative to the helix and loop portions is different owing to a very localized difference in backbone conformation. In alpha beta 1 connections, the chain enters the beta-strand via a residue adopting an extended conformation, while in alpha beta 3 it does so via a residue in a near alpha-helical conformation. Other conserved structural features include distinct patterns of side chain orientation relative to the beta-sheet surface and of main chain H-bonds in the loop and the beta-strand moieties. Significant differences also occur in packing interactions of conserved hydrophobic residues situated in the last turn of the helix. Yet the alpha-helix surface of both types of connections adopts similar orientations relative to the barrel sheet surface. Our results suggest furthermore that conserved hydrophobic residues along the sequence of the connections, may be correlated more with specific patterns of interactions made with neighboring helices and sheet strands than with helix/strand packing within the connection itself. A number of intriguing observations are also made on the distribution of the identified alpha beta 1 and alpha beta 3 loops within the alpha/beta-barrel motifs. They often occur adjacent to each other; alpha beta 3 loops invariably involve even numbered beta-strands, while alpha beta 1 loops involve preferentially odd beta-strands; all the analyzed proteins contain at least one alpha beta 3 loop in the first half of the eightfold alpha/beta barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel alpha/beta barrel motifs are discussed. 相似文献
74.
Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. 总被引:13,自引:0,他引:13
We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach. 相似文献
75.
The three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus dentrificans (PD-MADH) has been determined at 2.8 A resolution by the molecular replacement method combined with map averaging procedures, using data collected from an area detector. The structure of methylamine dehydrogenase from Thio-bacillus versutus, which contains an "X-ray" sequence, was used as the starting search model. MADH consists of 2 heavy (H) and 2 light (L) subunits related by a molecular 2-fold axis. The H subunit is folded into seven four-stranded beta segments, forming a disk-shaped structure, arranged with pseudo-7-fold symmetry. A 31-residue elongated tail exists at the N-terminus of the H subunit in MADH from T. versutus but is partially digested in this crystal form of MADH from P. denitrificans, leaving the H subunit about 18 residues shorter. Each L subunit contains 127 residues arranged into 10 beta-strands connected by turns. The active site of the enzyme is located in the L subunit and is accessible via a hydrophobic channel between the H and L subunits. The redox cofactor of MADH, tryptophan tryptophylquinone is highly unusual. It is formed from two covalently linked tryptophan side chains at positions 57 and 107 of the L subunit, one of which contains an orthoquinone. 相似文献
76.
Neurons require a large amount of intracellular transport. Cytoplasmic polypeptides and membrane-bounded organelles move from
the perikaryon, down the length of the axon, and to the synaptic terminals. This movement occurs at distinct rates and is
termed axonal transport. Axonal transport is divided into the slow transport of cytoplasmic proteins including glycolytic
enzymes and cytoskeletal structures and the fast transport of membrane-bounded organelles along linear arrays of microtubules.
The polypeptide compositions of the rate classes of axonal transport have been well characterized, but the underlying molecular
mechanisms of this movement are less clear. Progress has been particularly slow toward understanding force-generation in slow
transport, but recent developments have provided insight into the molecular motors involved in fast axonal transport. Recent
advances in the cellular and molecular biology of one fast axonal transport motor, kinesin, have provided a clearer understanding
of organelle movement along microtubules. The availability of cellular and molecular probes for kinesin and other putative
axonal transport motors have led to a reevaluation of our understanding of intracellular motility. 相似文献
77.
The degree of intergradation between two species of Sulawesi macaques,Macaca tonkeana andM. hecki, was studied by examining the diagnostic external characteristics of more than 100 monkeys kept as pets by natives. Two possible
hybrid monkeys were found and both originated from the borderland between the two species, located in the most proximal region
of the northern peninsula of Sulawesi. The previously postulated wide area of integradation between the two species at the
possible contact zone was, however, not recognized, and typical examples oftonkeana orhecki were found to be present on the two sides of a narrow “hybrid” zone which was defined by direct observations. Furthermore,
despite considerable individual variations, we were able to allocate most monkeys to one or other of the species. Each of
ten external characteristics of the members of both species more or less encompassed the individual variations, but may undergo
changes with the development of the monkeys. The mechanisms of reproduction of hybrid monkeys and the maintenance of differences
between the species are discussed. 相似文献
78.
Kunio Watanabe Shuichi Matsumura Tsuyoshi Watanabe Yuzuru Hamada 《Primates; journal of primatology》1991,32(3):385-389
Morphological observations of pet and wild monkeys were made in the area that was inferred to be the borderland betweenMacaca tonkeana andM. ochreata in Sulawesi. Almost all individual monkeys could be classified into one of two species by their external characteristics.
The possible borderland was estimated to extend from the La River in the east and to around Karaena River in the west. These
two species may make contact in the forest in the western area of the borderland. Some external characteristics exhibited
wide individual variations in the two species. Some monkeys originating from the borderland showed external characteristics
that were intermediate between those of the two species. The possible intergradation between these two species is discussed
in terms of the morphological variations found in the two species. 相似文献
79.
A. A. Serikov 《Journal of biological physics》1991,18(1):65-77
Model equations for the kinetics of the synthesis and decay of molecular aggregates are used to show the high sensitivity of equilibrium concentrations of high-molecular aggregates to external radiation. This phenomenon is used to explain the effects of low-intensity microwave fields on the functioning of biological systems. The experimental results on the influence of SHF-radiation on ferricyanide reduction by erythrocytes are interpreted in detail. 相似文献
80.