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L Holm

Publications and source records attributed to L Holm.

At least 109 records · Page 6Linked to original sources
PubMed1995

3-D lookup: fast protein structure database searches at 90% reliability.

There are far fewer classes of three-dimensional protein folds than sequence families but the problem of detecting three-dimensional similarities is NP-complete. We present a novel heuristic for identifying 3-D similarities between a query structure and the database of known protein structures. Many methods for structure alignment use a bottom-up approach, identifying first local matches and then solving a combinatorial problem in building up larger clusters of matching substructures. Here, the top-down approach is to start with the global comparison and select a rough superimposition using a fast 3-D lookup of secondary structure motifs. The superimposition is then extended to an alignment of C alpha atoms by an iterative dynamic programming step. An all-against-all comparison of 385 representative proteins (150,000 pair comparisons) took 1 day of computer time on a single R8000 processor. In other words, one query structure is scanned against the database in a matter of minutes. The method is rated at 90% reliability at capturing statistically significant similarities. It is useful as a rapid preprocessor to a comprehensive protein structure database search system.

Amino Acid Sequence↗
PubMed1994

The immunoglobulin fold. Structural classification, sequence patterns and common core.

Since the first crystal structure of an immunoglobulin revealed a modular architecture, the characteristic beta-sheet fold of the immunoglobulin domain has been found in many other proteins of diverse biological function. Here, a systematic comparison of 23 Ig domain structures with less than 25% pairwise residue identity was performed using automatic structural alignment and analysis of beta-sheet and loop topology. Sequence consensus patterns were identified for nine distinct families with at most marginal similarity to each other. The analysis reveals a common structural core of only four beta-strands (b, c, e and f), embedded in an antiparallel curled beta-sheet sandwich with a total of three to five additional strands (a, c', c'', d, g) and a characteristic intersheet angle. The variation in the position of the edge strands (a, c', c'', d and g) relative to the common core defines four different topological subtypes that correlate with the length of the intervening sequence between strands c and e, the most variable region in sequence. The switch of strand c' from one sheet to the other in seven-stranded domains appears to result from short c-e segments, rather than being a major structural discriminator. The high degree of structural flexibility outside the common core and the extreme variability of side-chain packing inside the core do not support a protein folding pathway common to all members of the structural class. Mutation rates of immunoglobulin-like domains in different proteins vary considerably. Disulfide bridges, thought to contribute to structural stability, are not necessarily invariant in number and location within a subclass.

Amino Acid Sequence↗
PubMed1994

Structural similarity of plant chitinase and lysozymes from animals and phage. An evolutionary connection.

A search in the database of known three-dimensional protein structures with the structure of a plant endochitinase revealed a subtle but unambiguous similarity to lysozymes from animals and phages. An evolutionary connection between plant endochitinases and lysozymes is supported by similar overall topology of fold, overlapping substrate specificities and remarkable conservation of some sequence and architectural detail around the active site. Much of the knowledge about lysozyme can now be extended by analogy to endochitinase. New insights into the mechanism of endochitinase are expected to stimulate genetic engineering studies into plant defense mechanisms against pests and pathogens.

Amino Acid Sequence↗
PubMed1994

Searching protein structure databases has come of age.

The number of protein structures known in atomic detail has increased from one in 1960 (Kendrew, J.C., Strandberg, B.E., Hart, R.G., Davies, D.R., Phillips, D.C., Shore, V.C. Nature (London) 185:422-427, 1960) to more than 1000 in 1994. The rate at which new structures are being published exceeds one a day as a result of recent advances in protein engineering, crystallography, and spectroscopy. More and more frequently, a newly determined structure is similar in fold to a known one, even when no sequence similarity is detectable. A new generation of computer algorithms has now been developed that allows routine comparison of a protein structure with the database of all known structures. Such structure database searches are already used daily and they are beginning to rival sequence database searches as a tool for discovering biologically interesting relationships.

Algorithms↗
PubMed1994

Parser for protein folding units.

General patterns of protein structural organization have emerged from studies of hundreds of structures elucidated by X-ray crystallography and nuclear magnetic resonance. Structural units are commonly identified by visual inspection of molecular models using qualitative criteria. Here, we propose an algorithm for identification of structural units by objective, quantitative criteria based on atomic interactions. The underlying physical concept is maximal interactions within each unit and minimal interaction between units (domains). In a simple harmonic approximation, interdomain dynamics is determined by the strength of the interface and the distribution of masses. The most likely domain decomposition involves units with the most correlated motion, or largest interdomain fluctuation time. The decomposition of a convoluted 3-D structure is complicated by the possibility that the chain can cross over several times between units. Grouping the residues by solving an eigenvalue problem for the contact matrix reduces the problem to a one-dimensional search for all reasonable trial bisections. Recursive bisection yields a tree of putative folding units. Simple physical criteria are used to identify units that could exist by themselves. The units so defined closely correspond to crystallographers' notion of structural domains. The results are useful for the analysis of folding principles, for modular protein design and for protein engineering.

Actins↗
PubMed1994

Hydrogen ion concentration in the mucus layer on top of acid-stimulated and -inhibited rat gastric mucosa.

BACKGROUND/AIMS: The gastric mucosa is covered by a continuous layer of bicarbonate-containing mucus gel; the question arises how acid, formed in the gastric glands, moves into the lumen. METHODS: The pH in the gastric mucus gel and gel thickness were measured in anesthetized rats with pH-sensitive microelectrodes (tip diameter, 1-5 microns). RESULTS: During pentagastrin (40 micrograms.kg-1.h-1) stimulation of acid secretion, the pH was higher in the gel than in the lumen (pH 2) up to a distance of 115 +/- 18 microns from the epithelial surface and maximal (pH 7.2 +/- 0.1) at the surface. A similar pH gradient was recorded at luminal pH 3. After omeprazole (10 mumol/kg) inhibition of endogenous acid secretion and with exogenous acid in the lumen, the pH profile was broader: 204 +/- 26 microns at luminal pH 2 and 231 +/- 63 microns at luminal pH 3. In contrast, the pH at the epithelial surface was lower (pH 6.8-6.9). The gel thickness (200-300 microns) was similar in all groups. CONCLUSIONS: The significantly higher surface pH in acid-secreting stomachs probably reflects better availability of interstitial mucosal bicarbonate. Bulk transport of secreted acid in channels created by the gland luminal hydrostatic pressure may additionally act to limit acidification of the mucus gel.

Animals↗
PubMed1994

LexA repressor and iron uptake regulator from Escherichia coli: new members of the CAP-like DNA binding domain superfamily.

Comparison of structures can reveal surprising connections between protein families and provide new insights into the relationship between sequence, structure and function. The solution structure of LexA repressor from Escherichia coli reveals an unexpected structural similarity to a widespread class of prokaryotic and eukaryotic regulatory proteins, which is typified by catabolite gene activator protein (CAP). The use of combined sequence profiles allows the identification of two new prokaryotic members of the superfamily: listeriolysin regulatory protein (PrfA) and ferric uptake regulatory protein (Fur). LexA, PrfA and Fur are the first examples of prokaryotic regulatory proteins in which DNA recognition is mediated by a variant of the classical helix-turn-helix motif, with an insertion in the turn region.

Amino Acid Sequence↗
PubMed1994

Histamine is not involved in pentagastrin-induced gastric mucosal vasodilation in the rat.

The effects of histamine and its role in the gastric mucosal vascular response to pentagastrin were studied in anesthetized rats. Blood flow was measured with laser-Doppler flowmetry (LDF) and with red blood cell velocity measurements in the superficial mucosal microcirculation. Acid secretion was determined by titration of the saline covering 0.8 cm2 of the fundic mucosa. Pentagastrin (40 micrograms.kg-1 x h-1 i.v. induced a blood flow increase (+40%), which was not significantly altered by ranitidine (H2-receptor antagonist, 2 mg/kg iv bolus), whereas the stimulated acid output was abolished. In experiments in which the H1-receptor antagonist pyrilamine (2.5 mg/kg i.v. bolus) was administered before pentagastrin stimulation, pentagastrin still increased blood flow by approximately 60%. Intravenous histamine (4 mg.kg-1 x h-1) induced a blood flow reduction in parallel with the reduction in blood pressure (vascular resistance unchanged). Even during intra-arterial (thoracic aorta) infusion of histamine (1 or 4 mg.kg-1 x h-1), gastric vascular resistance was unchanged. In animals pretreated with pyrilamine, histamine (4 mg.kg-1 x h-1 i.v.) left the gastric blood flow and blood pressure unchanged. These results indicate that the pentagastrin-induced increase in the rat gastric blood flow is not dependent on histamine.

Animals↗
PubMed1994

Exposure of the duodenum to high concentrations of hydrochloric acid. Effects on mucosal permeability, alkaline secretion, and blood flow.

Proximal duodenum was perfused with HCl for 5 min and the effects on blood-to-lumen clearance of 51Cr-EDTA (ED-Cl), morphology, luminal alkalinization, and blood flow determined in anesthetized rats. The rate of alkalinization was determined by back titration and blood flow assessed by laser Doppler flowmetry or by ultrasonic transit time flowmetry. Perfusion of duodenum with 30, 50 or 100 mM HCl for 5 min increased ED-Cl in a concentration-dependent manner and induced a small increase in alkalinization but had no effect on blood flow. At 55 min after cessation of perfusion with 100 mM HCl ED-Cl was 2.2-fold higher than control whereas the ED-Cl values in animals perfused with 30 or 50 mM HCl were not different from pre-acid control values. 100 mM HCl also induced an increase in 14C-mannitol and 14C-polyethylene glycol 4000 clearance, suggesting that HCl does indeed increase mucosal permeability. The 100 mM HCl-induced rise in mucosal permeability most probably reflects disturbance of mucosal integrity because three of five animals exhibited villous tip damage. The increases in ED-Cl in response to 100 mM HCl were the same in control rats as in rats with the renal pedicles ligated, indicating that the acid susceptibility is not affected by acute functional nephrectomy.

Alkalies↗
PubMed1994

The FSSP database of structurally aligned protein fold families.

FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB). The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (remote homologs, < 30% sequence identity), as well as all structures in the Protein Data Bank with 70-30% sequence identity relative to the search structure (medium homologs). Very close homologs (above 70% sequence identity) are excluded as they rarely have marked structural differences. The alignments of remote homologs are the result of pairwise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based purely on the 3D co-ordinates of the proteins and are derived by automatic (objective) structure comparison programs. The significance of structural similarity is estimated based on statistical criteria. The FSSP database is available electronically from the EMBL file server and by anonymous ftp (file transfer protocol).

Amino Acid Sequence↗
PubMed1993

Protein structure comparison by alignment of distance matrices.

With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residue-residue (C alpha-C alpha) distance matrices. The distance matrices are first decomposed into elementary contact patterns, e.g. hexapeptide-hexapeptide submatrices. Then, similar contact patterns in the two matrices are paired and combined into larger consistent sets of pairs. A Monte Carlo procedure is used to optimize a similarity score defined in terms of equivalent intramolecular distances. Several alignments are optimized in parallel, leading to simultaneous detection of the best, second-best and so on solutions. The method allows sequence gaps of any length, reversal of chain direction and free topological connectivity of aligned segments. Sequential connectivity can be imposed as an option. The method is fully automatic and identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions. An all-against-all alignment of over 200 representative protein structures results in an objective classification of known three-dimensional folds in agreement with visual classifications. Unexpected topological similarities of biological interest have been detected, e.g. between the bacterial toxin colicin A and globins, and between the eukaryotic POU-specific DNA-binding domain and the bacterial lambda repressor.

Actins↗
PubMed1993

Structural alignment of globins, phycocyanins and colicin A.

A database search employing a novel algorithm for protein structure comparison by alignment of distance matrices has revealed a striking resemblance between the tertiary structures of the bacterial toxin colicin A and globins. The globin-like domain in colicin A contains all elements essential for the toxin's lethal ionophoric activity. The structural similarity between colicin A and globins is comparable to that between globins and phycocyanins. This suggests that these three protein families, which have unrelated sequences and different functional contexts, are an example of physical convergence to a stable folding motif, the three-on-three helical sandwich.

Amino Acid Sequence↗
PubMed1993

A randomized study of neuropsychological function in patients undergoing coronary bypass surgery.

Fifty-four male patients were examined by an extensive battery of neuropsychological tests before and 1 and 6 months after coronary artery surgery. The patients were randomized to one of three methods of extracorporeal circulation (ECC): bubble oxygenation without an arterial line filter (Group I, n = 17), bubble oxygenation with an arterial filter (Group II, n = 17), or membrane oxygenation without an arterial filter (Group III, n = 20). The mean age was 59 (range 44-69) years. At 1 month nine patients (17%) and at 6 months four patients (7%) had neuropsychological deficits (reduction of 1 standard deviation in two or more tests). Postoperative intellectual dysfunction was found in groups I, II, and III at 1 and 6 months in 24% and 12%, 12% and 6%, and 15% and 5%, respectively. The differences between groups were not statistically significant. Significantly more patients in the membrane oxygenator group than in the bubble-oxygenator group without a filter performed better in the test for attention, visual scanning, and psychomotor speed and in the test for learning and memory at 1-month follow-up. In conclusion, there exists a risk of neuropsychological dysfunction after ECC, with improvement within the first 6 months, which is independent of the type of oxygenation and the use of arterial line filtration during ECC in this low-risk group.

Adult↗
PubMed1993

Vasoactive intestinal polypeptide reduces hydrochloric acid-induced duodenal mucosal permeability.

The duodenum in anesthetized rats was perfused with HCl, and mucosal integrity was assessed by measuring the clearance of 51Cr-labeled EDTA from blood to lumen and/or by morphological examination (lesion score). Duodenal blood flow was determined by laser Doppler flowmetry and luminal alkalinization as well as H+ disappearance by backtitration. Intravenous infusion of vasoactive intestinal polypeptide (VIP; 13.5 micrograms.kg-1.h-1) increased luminal alkalinization threefold and decreased clearance of 51Cr-EDTA by 50%. VIP also decreased arterial blood pressure and induced a small and irregular decrease in duodenal blood flow. Perfusion with 10 mM HCl increased clearance of 51Cr-EDTA 2.1-fold, but the lesion score was not different from that in saline-perfused animals. Perfusion with 20 mM HCl increased clearance of 51Cr-EDTA four-fold and induced a greater lesion score than did 10 mM. Perfusion with either 10 or 20 mM HCl did not affect the duodenal blood flow. VIP reduced the rise in clearance of 51Cr-EDTA in response to 10 mM but not that to 20 mM HCl. Intravenous injection of prazosin (50 micrograms/kg) decreased luminal alkalinization, clearance of 51Cr-EDTA, blood pressure, and duodenal blood flow. In prazosin-pretreated rats, perfusion with 10 mM HCl increased clearance of 51Cr-EDTA 2.6-fold, and the lesion score was greater in this group than in animals infused with VIP. A positive linear correlation was obtained between HCO3- secretion and the mean rate of H+ disappearance.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1993

Influence of tactile stimulation of the rat gastric mucosa on blood flow and acid output.

The influence of tactile stimulation of the gastric mucosa (mimics the mechanical influence of the food bolus) on the gastric mucosal blood flow and acid output was studied in rats anesthetized with Inactin. Blood flow was measured with laser-Doppler flowmetry (LDF) with the probe positioned above the gastric mucosa, and acid secretion was measured at regular intervals by titration of the saline covering 0.8 cm2 of the mucosa. After gentle tactile stimulation (wiping with cotton tips) of the mucosa for 20 s, blood flow increased to approximately 250% of the control value and then returned to the control level 15 min later, whereas acid output was transiently reduced immediately after tactile stimulation. Pretreatment with lidocaine, methysergide, or hexamethonium did not change the results of tactile stimulation on the blood flow. After indomethacin (3 mg/kg i.v.) LDF was significantly reduced by 33% and the hyperemic response to tactile stimulation was almost abolished. This suggests that endogenously released prostaglandins, not evoked through activation of intramural reflexes that can be blocked by lidocaine, methysergide or hexamethonium, are responsible for the hyperemia seen after tactile stimulation of the gastric mucosa.

Animals↗