Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “local structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources
PubMed1976

Fine structural localization of Concanavalin A binding sites on hamster spermatozoa.

The plasma membrane of epididymal spermatozoa of the golden hamster (Mesocricetus auratus) exhibits morphological differences over various parts of the head and tail as detected by air-dried replicas and freeze-etching techniques. In an attempt to ascertain whether any topographical differences exist in the number or distribution of carbohydrate moieties associated with the cell surface, cells were labeled with Concanavalin A and marked with hemocyanin. It was found that while the plasma membrane over the acrosomal region differed from that of the postacrosomal region in membrane components revealed by freeze fracturing, there was no apparent difference in the distribution or density of Con A binding sites detectable by hemocyanin localization. The tail regions exhibited differences in both fracture face appearance and the distribution of detectable carbohydrate moieties. It was also found that binding sites for Concanavalin A exist on the inner and outer acrosomal membranes in addition to those on the plasma membrane.

Acrosome↗
PubMed2004

Evaluation of local structure alphabets based on residue burial.

Residue burial, which describes a protein residue's exposure to solvent and neighboring atoms, is key to protein structure prediction, modeling, and analysis. We assessed 21 alphabets representing residue burial, according to their predictability from amino acid sequence, conservation in structural alignments, and utility in one fold-recognition scenario. This follows upon our previous work in assessing nine representations of backbone geometry.1 The alphabet found to be most effective overall has seven states and is based on a count of C(beta) atoms within a 14 A-radius sphere centered at the C(beta) of a residue of interest. When incorporated into a hidden Markov model (HMM), this alphabet gave us a 38% performance boost in fold recognition and 23% in alignment quality.

Amino Acids↗
PubMed2004

Detecting local structural similarity in proteins by maximizing number of equivalent residues.

A new algorithm for superimposing protein structures based on maximizing the number of spatially equivalent residues is introduced. The algorithm works in three distinct steps. First, the optimal residue map is calculated by structural alignment. By default, the double dynamic programming algorithm, as implemented in the program ASH, was used for the structure alignment step, but we also present results based on alignments imported from three other programs (Dali, CE, and VAST).Second, the structures are spatially superimposed such that the effective number of equivalent residues (NER)--aligned residue pairs that can be spatially overlapped--is maximized. The NER score is an analytic, differentiable similarity function that rewards spatially equivalent residues but ignores non-equivalent ones. Maximization of the NER score results in accurate superpositions in cases where root mean square deviation (RMSD) minimization fails. Third, the NER function is used in conjunction with traditional dynamic programming to realign the structures based on the proximity of residues in the superposition. Results are presented for a wide range of superposition problems and compared to results from Dali, CE, and VAST. In addition, several structure-structure pairs that show only partial similarity are discussed, and results are compared to those from the LGA, SARF2, and ThreeCa programs.

Algorithms↗
PubMed1993

Molluscan chymotrypsin-like protease: structure, localization, and substrate specificity.

A messenger RNA encoding a chymotrypsin-like preproprotease is expressed abundantly and specifically in the distal quarter of the intestine of the mollusc Haliotis rufescens (red abalone). Consistent with this finding, a chymotrypsin-like activity was detected at highest concentration in the lumen of this segment of the intestine. Because the complexity of total protein in the distal intestinal fluid was low and the chymotrypsin-like protease was highly expressed, purification of the enzyme to near homogeneity was achieved by a single passage over an anion-exchange resin. The primary specificity of the protease, predicted from homology of the key amino acid residues (Ser189, Gly216, and Ser226) in the substrate binding site with similar residues lining the S1 subsites of other chymotrypsin-like enzymes, was confirmed by hydrolysis of a family of tetrapeptide substrates with different P1 amino acids. The optimal P1 residues include those with bulky, gamma-branched side chains (phenylalanine and leucine) similar to the side chain of the asparagine residue at P1 of the activation peptide of the proenzyme. Thus, unlike zymogens of the pancreatic serine proteases, which are activated by the common tryptic mechanism, the zymogen of the molluscan enzyme appears to be activated by an autocatalytic mechanism, i.e., by cleavage with active chymotrypsin-like protease. Additional unique properties of the enzyme predicted from the primary sequence include an unpaired cysteine, with the potential for internal thiol-disulfide isomerization between two different conformers of the protease.

Amino Acid Sequence↗
PubMed1995

Structure, localization, and molecular phylogeny of a GnRH cDNA from a paracanthopterygian fish, the plainfin midshipman (Porichthys notatus).

Multiple forms of gonadotropin releasing hormone (GnRH) are found within several species of teleost fishes. Within the infradivision Euteleostei, the superorder Paracanthopterygii represents one of the last major groups to be examined with respect to the GnRH mRNA sequence. The plainfin midshipman, Porichthys notatus, is a common member of this superorder which is intermediate between the ancestral euteleost taxa and the more derived Acanthopterygians (percomorphs). The goals of this study were to: (1) determine the cDNA sequence of prepro-GnRH in the plainfin midshipman, (2) address the anatomical localization of midshipman prepro-GnRH gene expression, and (3) perform a cladistic analysis using all currently known cDNA sequences of prepro-GnRH. We report 460 base pair of cDNA sequence containing the entire protein coding region, and 5'- and 3'-untranslated regions. The deduced amino acid sequence indicates that this cDNA encodes a GnRH decapeptide identical in sequence to that originally isolated in salmon (Trp7, leu8 - GnRH). Northern analysis demonstrated transcripts in brain, ovary, and testis (600-700 nucleotides). PCR showed that the ovarian prepro-GnRH was identical to that found in brain. In situ hybridization labeled neurons in the ganglion of the terminal nerve and the preoptic area, forebrain areas previously observed to contain GnRH-like immunoreactivity. Last, a phylogenetic analysis of 18 prepro-GnRH sequences grouped the Paracanthopterygii with the Acanthopterygii. However, this recent clade was distinct from two separate and more ancestral lineages, the Paracanthopterygii (salmonids) and Ostariophysi (represented by catfish).

Amino Acid Sequence↗
PubMed1997

The human TRIDENT/HFH-11/FKHL16 gene: structure, localization, and promoter characterization.

We recently identified the winged-helix/fork head transcription factor Trident in mouse and described its expression in cycling cells. Here we report the isolation and characterization of the human TRIDENT (HGMW-approved symbol FKHL16) cDNA and gene. Homology between the human and the mouse Trident proteins was 79%. The gene consists of 10 exons and is located on chromosome 12 band p13. The winged-helix DNA-binding domain is encoded on three exons. Analysis of the promoter in synchronized Rat-1 fibroblasts revealed a fragment of 300 bases responsible for the cell cycle-specific expression of the TRIDENT gene.

Amino Acid Sequence↗
PubMed1999

Correlation of observed fold frequency with the occurrence of local structural motifs.

It is well known that some protein folds (superfolds) occur very frequently. We show that compared to other folds, most superfold structures have a higher proportion of their alpha-helical or beta-strand residues in one of three basic units of supersecondary structure (alpha-hairpin, beta-hairpin or betaalphabeta-unit). Furthermore, by taking into consideration two more complex motifs, the four-stranded Greek-key (beta4) and the betaalpha-Greek key (betaalphabetabeta), we demonstrate that the remaining superfold structures contain many of these higher order units of three-dimensional packing. The implications of these results for folding are discussed.

Models, Molecular↗
PubMed1991

Immunogold fine structural localization of extracellular matrix components in aged human cornea. II. Collagen types V and VI.

Using immunogold immunocytochemical techniques we studied the distribution of collagen types V and VI in corneal tissue from seven enucleated human eyes (age range, 63-78 years). Results obtained by cryoultramicrotomy were marginally more intense than those obtained using London Resin white (LR white) embedding. Type V collagen was present in the striated collagen fibrils in Bowman's layer, in the stroma and in a thin, non-banded anterior zone of Descemet's membrane. Our results suggest that types I, III and V collagen co-distribute in striated collagen fibrils. By contrast, type VI collagen was located in fine filaments in the interfibrillar matrix of the stroma, in Bowman's layer and in the anchoring plaques of the sub-epithelial basement-membrane complex. This implies an importance in epithelial adhesion which was previously unsuspected. Keratocyte bodies were electron-dense, amorphous extracellular deposits of matrix-like material, and these were labelled with types III, V and VI collagen antibodies. Long-spacing collagen was observed in the corneal stroma, and this deposit did not contain any of the collagen types studied.

Aged↗
PubMed1988

Fine-structural localization of neuropeptide tyrosine (NPY)-like immunoreactivity in the neuronal somata of colchicine-pretreated celiac ganglia of rats.

In colchicine-pretreated cells of sympathetic ganglia, intensely NPY-immunoreactive material was localized within vacuoles and vesicles of the disorganized, widely dispersed Golgi apparatus. Intensely positive large granular vesicles, which are known to be one of major storage sites of various peptides in the autonomic nerve endings, were essentially unobserved in the perikaryal cytoplasm. The present finding provides evidence that one pool of NPY-like immunoreactivity is localized in the Golgi apparatus of colchicine-pretreated as well as normal sympathetic ganglion cells. It is also clear that visualization of NPY-immunoreactive somata by colchicine-pretreatment in the sympathetic ganglia is due to the accumulation of the neuropeptide in the disorganized Golgi stacks instead of increased amount of the large granular vesicles containing NPY.

Animals↗
PubMed1978

The fine structural localization of acetylcholinesterase in the muscle spindle of the rat.

Muscle spindles from lumbricalis muscles of the rat were incubated for acetylcholinesterase with a modified thiocholine-method of Lewis and Shute and examined by light ane electron microscopy. All types of motor nerve ending showed heavy deposits of reaction product in the synaptic cleft. The underlying sarcoplasmic reticulum, transverse tubular system, and, when present, the envelope of sole plate nuclei were also stained. In the sensory region, the reaction was negative in the interface between the plasma membranes of the primary sensory terminal and muscle. One of two secondary sensory endings identified showed distinct reaction product in the cleft; the other secondary sensory ending showed no such reaction. Precipitates were present on the sarcolemma of the intrafusal muscle fibers in the polar and adjacent myotube regions, but not at the spindle equator. Extrafusal and intrafusal myelinated gamma-nerve fibers and preterminal motor axons showed staining of the axolemma. Fibers with thick myelin sheaths and preterminal sensory axons were free of acetylcholinesterase activity, as were the unmyelinated nerve fibers.

Acetylcholinesterase↗
PubMed1976

The fine structural localization of testicular phosphatases in man: the control testis.

Electron microscopic cytochemistry was used to determine the localization of five phosphatase enzymes-glucose-6-phosphatase, inosine diphosphatase, thiamine pyrophosphatase, acid phosphatase, and adenosine triphosphatase-in control human testes. Glucose-6-phosphatase occurred in the endoplasmic reticulum and nuclear envelope of Sertoli cells, Leydig cells and primitive spermatogonia, but was not observed in more advanced spermatogenic cells. The presence of glucose-6-phosphatase activity paralleled the presence of glycogen in spermatogenic cells, i.e., both occurred in type AL and AD spermatogonia but not in type AP or B spermatogonia or in more advanced spermatogenic cells. Inosine diphosphatase activity was found in the endoplasmic reticulum, nuclear envelope, and Golgi complex of Sertoli cells and all spermatogenic cells except late spermatids. Additionally, inosine diphosphatase activity was localized at the junctions between Sertoli cells and late spermatids, but was not associated with any other plasma membrane. Thiamine pyrophosphatase reaction product was found in the Golgi bodies of Sertoli cells and in spermatogenic cells through immature spermatids. Neither inosine diphosphatase nor thiamine pyrophosphatase was observed in the Golgi bodies of spermatids during acrosomal formation. Acid phosphatase activity was found in lysosomes of spermatogonia, spermatocytes, and spermatids, in lysosomes of Leydig cells, and in lysosomes, lipofuscin bodies, and Golgi cisternae of Sertoli cells. It is thought that Sertoli lysosomes play a role in the phagocytosis of degenerating germ cells; however, the role of spermatogenic or Leydig lysosomes is unknown. Adenosine triphosphatase activity occurred at the interfaces between two spermatogonia, and between Sertoli cells and spermatogonia, but was not observed in the spaces between two Sertoli cells, two spermatocytes, two spermatids, or between Sertoli cells and spermatocytes, or between Sertoli cells and spermatids.

Acid Phosphatase↗