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A Sali

Publications and source records attributed to A Sali.

At least 91 records · Page 5Linked to original sources
PubMed1995

Autophosphorylation of PC-1 (alkaline phosphodiesterase I/nucleotide pyrophosphatase) and analysis of the active site.

PC-1 is an ecto-enzyme possessing alkaline phosphodiesterase I (EC 3.1.4.1) and nucleotide pyrophosphatase (EC 3.6.1.9) activities. It has also been proposed to be an ecto-protein kinase capable of phosphorylating itself as well as exogenous proteins. We have investigated the phosphorylation capability of PC-1 and have developed a novel method for its detection and characterization based on autophosphorylation, which allows detection without the use of antibodies. When cells expressing membrane PC-1 were held on ice with [gamma-32P]ATP, SDS/PAGE of whole cell lysates showed a single band which was PC-1; this band was absent in cells not expressing PC-1. Immunoprecipitates of soluble PC-1 isolated from culture supernatants of cells expressing PC-1 were also capable of autophosphorylation, and the size of the labeled protein was the same as previously reported for soluble PC-1. PC-1 was also labeled with [alpha-32P]ATP and [35S]dATP[alpha S]. We found no evidence that PC-1 was capable of phosphorylating proteins other than itself, and conclude that it is not a true kinase, and that the observed labeling with [gamma-32P]ATP, [alpha-32P]ATP and [35S]dATP[alpha S] reflect transient covalent adducts that are part of the catalytic cycle of phosphodiesterase/pyrophosphatase activity rather than intrinsic kinase activity. Mutation of the active-site threonine to tyrosine, serine or alanine reduced the 5'-nucleotide phosphodiesterase activity of PC-1 and its ability to autophosphorylate to undetectable levels. Together, these data suggest that both activities depend on the same site.

Adenosine Triphosphate↗
PubMed1995

Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk.

BACKGROUND: Proline-rich segments in the guanine nucleotide exchange factor C3G bind much more strongly to the N-terminal Src homology 3 domain (SH3-N) of the proto-oncogene product c-Crk than to other SH3 domains. The presence of a lysine instead of an arginine in the peptides derived from C3G appears to be crucial for this specificity towards c-Crk. RESULTS: In order to understand the chemical basis of this specificity we have determined the crystal structure of Crk SH3-N in complex with a high affinity peptide from C3G (PPPALPPKKR, Kd approximately 2 microM) at 1.5 A resolution. The peptide adopts a polyproline type II helix that binds, as dictated by electrostatic complementarity, in reversed orientation relative to the orientation seen in the earliest structures of SH3-peptide complexes. A lysine in the C3G peptide is tightly coordinated by three acidic residues in the SH3 domain. In contrast, the co-crystal structure of c-Crk SH3-N and a peptide containing an arginine at the equivalent position (determined at 1.9 A resolution) reveals non-optimal geometry for the arginine and increased disorder. CONCLUSIONS: The c-Crk SH3 domain engages in an unusual lysine-specific interaction that is rarely seen in protein structures, and which appears to be a key determinant of its unique ability to bind the C3G peptides with high affinity.

Amino Acid Sequence↗
PubMed1995

Evaluation of comparative protein modeling by MODELLER.

We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for comparative protein modeling by satisfaction of spatial restraints. The models have good stereochemistry and are at least as similar to the crystallographic structures as the closest template structures. The largest errors occur in the regions that were not aligned correctly or where the template structures are not similar to the correct structure. These regions correspond predominantly to exposed loops, insertions of any length, and non-conserved side chains. When a template structure with more than 40% sequence identity to the target protein is available, the model is likely to have about 90% of the mainchain atoms modeled with an rms deviation from the X-ray structure of approximately 1 A, in large part because the templates are likely to be that similar to the X-ray structure of the target. This rms deviation is comparable to the overall differences between refined NMR and X-ray crystallography structures of the same protein.

Amino Acid Sequence↗
PubMed1995

Modeling mutations and homologous proteins.

A protein sequence with at lease 40% identity to a known structure can now be modelled automatically, with an accuracy approaching that o fa low-resolution X-ray structure or a medium-resolution nuclear magnetic resonance structure. In general, these models have goods stereochemistry and an overall structural accuracy that is as high as the similarity between the template and the actual structure being predicted. As a result, the number of sequences that can be modelled is an order of magnitude larger then the number of experimentally determined protein structures. In addition, evaluation techniques are available that can estimated errors in different regions of the model. Thus, the number of applications where homology modelling is proving useful is growing rapidly.

Amino Acid Sequence↗
PubMed1995

Theoretical studies of protein folding and unfolding.

The mechanism of protein folding is being investigated theoretically by the use of both simplified and all-atom models of the polypeptide chain. Lattice heteropolymer simulations of the folding process have led to proposals for the folding mechanism and for the resolution of the Levinthal paradox. Both stability and rapid folding have been shown in model studies to result from the presence of a pronounced global energy minimum corresponding to the native state. Concomitantly, molecular dynamics simulations with detailed atomic models have been used to analyze the initial stages of protein unfolding. Results concerning possible folding intermediates and the role of water in the unfolding process have been obtained. The two types of theoretical approaches are providing information essential for an understanding of the mechanism of protein folding and are useful for the design of experiments to study the mechanism in different proteins.

Models, Theoretical↗
PubMed1995

Comparative protein modeling by satisfaction of spatial restraints.

Approximately one third of known protein sequences are related to at least one known protein structure. As a result, an order of magnitude more sequences can be modeled by comparative modeling than there are experimentally determined protein structures. A large fraction of these models has an accuracy approaching that of a low resolution X-ray structure or a medium resolution nuclear magnetic resonance structure. The number of applications where homology modeling has been proven useful is growing rapidly.

Amino Acid Sequence↗
PubMed1995

Choledochoplasty for cholecystocholedochal fistula (Mirizzi syndrome type II): a case report and literature review.

The following is a case report of a cholecystocholedochal fistula (Mirizzi syndrome Type II) in a 61 year old woman. The use of a pedicled graft of gall-bladder remnant in the treatment of this condition is presented. If the condition is recognized early, bile duct injury can be prevented and the need for more complex techniques of bile duct repair or bypass may be averted.

Bile Duct Diseases↗
PubMed1994

Divalent cations stabilize the conformation of plasma cell membrane glycoprotein PC-1 (alkaline phosphodiesterase I).

The plasma cell-membrane glycoprotein PC-1 is an ectoenzyme with alkaline phosphodiesterase I/5'-nucleotide phosphodiesterase (EC 3.1.4.1) and nucleotide pyrophosphatase (EC 3.6.1.9) activities. It contains sequence motifs which closely match the consensus EF-hand (helix-loop-helix) Ca(2+)-binding regions of parvalbumin, troponin-C and calmodulin, and its enzymic activity is increased in the presence of divalent cations and decreased in the presence of chelating agents. We have undertaken experiments to determine whether divalent cations affect the conformation of the PC-1 protein, as assessed by their effect on thermal stability, resistance to proteolysis and binding of polyclonal antibodies to the whole native protein and monoclonal antibodies to a putative Ca(2+)-binding region. Divalent cations were found to protect solubilized PC-1 against thermal denaturation and proteolysis. They also stabilized PC-1 on intact cells; this form was much more resistant to proteolysis than Triton X-100 solubilized PC-1. Ca2+, Mg2+ and Zn2+ ions were equally effective. Monoclonal antibodies to the bacterially expressed C-terminal EF-hand homology region only bound to mammalian PC-1 in the absence of Ca2+. In contrast, the great majority of polyclonal antibodies to native PC-1 bound regardless of whether Ca2+ was present or not, but with increased binding when Ca2+ was present. These results provide evidence that divalent cations bind to PC-1 and stabilize its conformation.

Amino Acid Sequence↗
PubMed1994

How does a protein fold?

The number of all possible conformations of a polypeptide chain is too large to be sampled exhaustively. Nevertheless, protein sequences do fold into unique native states in seconds (the Levinthal paradox). To determine how the Levinthal paradox is resolved, we use a lattice Monte Carlo model in which the global minimum (native state) is known. The necessary and sufficient condition for folding in this model is that the native state be a pronounced global minimum on the potential surface. This guarantees thermodynamic stability of the native state at a temperature where the chain does not get trapped in local minima. Folding starts by a rapid collapse from a random-coil state to a random semi-compact globule. It then proceeds by a slow, rate-determining search through the semi-compact states to find a transition state from which the chain folds rapidly to the native state. The elements of the folding mechanism that lead to the resolution of the Levinthal paradox are the reduced number of conformations that need to be searched in the semi-compact globule (approximately 10(10) versus approximately 10(16) for the random coil) and the existence of many (approximately 10(3)) transition states. The results have evolutionary implications and suggest principles for the folding of real proteins.

Models, Chemical↗
PubMed1994

Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.

A three-dimensional lattice model of a protein is used to investigate the properties required for its folding to the native state. The polypeptide chain is represented as a 27 bead heteropolymer whose lowest energy (native) state can be determined by an exhaustive enumeration of all fully compact conformations. A total of 200 sequences with random interactions are generated and subjected to Monte Carlo simulations to determine which chains find the ground state in a short time; i.e. which sequences overcome the folding problem referred to as the Levinthal paradox. Comparison of the folding and non-folding sequences is used to identify the features that are required for fast folding to the global energy minimum. It is shown that successful folding does not require certain attributes that have been previously proposed as necessary for folding; these include a high number of short versus long-range contacts in the native state, a high content of the secondary structure in the native state, a strong correlation between the native contact map and the interaction parameters, and the existence of a high number of low energy states with near-native conformation. Instead, the essential difference between the folding and the non-folding sequences is the nature of the energy spectrum. The necessary and sufficient condition for a sequence to fold rapidly in the present model is that the native state is a pronounced energy minimum. As a consequence, the thermodynamic stability of the native state of a folding sequence has a sigmoidal dependence on temperature. This permits such a sequence to satisfy both the thermodynamic and the kinetic requirements for folding; i.e. the native state predominates thermodynamically at temperatures that are high enough for folding to be kinetically possible. The applicability of the present results to real proteins is discussed.

Algorithms↗
PubMed1994

Derivation of rules for comparative protein modeling from a database of protein structure alignments.

We describe a database of protein structure alignments as well as methods and tools that use this database to improve comparative protein modeling. The current version of the database contains 105 alignments of similar proteins or protein segments. The database comprises 416 entries, 78,495 residues, 1,233 equivalent entry pairs, and 230,396 pairs of equivalent alignment positions. At present, the main application of the database is to improve comparative modeling by satisfaction of spatial restraints implemented in the program MODELLER (Sali A, Blundell TL, 1993, J Mol Biol 234:779-815). To illustrate the usefulness of the database, the restraints on the conformation of a disulfide bridge provided by an equivalent disulfide bridge in a related structure are derived from the alignments; the prediction success of the disulfide dihedral angle classes is increased to approximately 80%, compared to approximately 55% for modeling that relies on the stereochemistry of disulfide bridges alone. The second example of the use of the database is the derivation of the probability density function for comparative modeling of the cis/trans isomerism of the proline residues; the prediction success is increased from 0% to 82.9% for cis-proline and from 93.3% to 96.2% for trans-proline. The database is available via electronic mail.

Amino Acid Sequence↗
PubMed1993

Comparative protein modelling by satisfaction of spatial restraints.

We describe a comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures. The three-dimensional (3D) model is obtained by optimally satisfying spatial restraints derived from the alignment and expressed as probability density functions (pdfs) for the features restrained. For example, the probabilities for main-chain conformations of a modelled residue may be restrained by its residue type, main-chain conformation of an equivalent residue in a related protein, and the local similarity between the two sequences. Several such pdfs are obtained from the correlations between structural features in 17 families of homologous proteins which have been aligned on the basis of their 3D structures. The pdfs restrain C alpha-C alpha distances, main-chain N-O distances, main-chain and side-chain dihedral angles. A smoothing procedure is used in the derivation of these relationships to minimize the problem of a sparse database. The 3D model of a protein is obtained by optimization of the molecular pdf such that the model violates the input restraints as little as possible. The molecular pdf is derived as a combination of pdfs restraining individual spatial features of the whole molecule. The optimization procedure is a variable target function method that applies the conjugate gradients algorithm to positions of all non-hydrogen atoms. The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases.

Amino Acid Sequence↗
PubMed1993

Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan binding regions and protease-specific antigenic epitopes.

Mouse mast cell protease (mMCP) 1, mMCP-2, mMCP-4, and mMCP-5 are serine proteases which are predicted to have chymotryptic specificity (chymases). They are bound to negatively charged heparin or chondroitin sulfate proteoglycans and are stored in secretory granules. Three-dimensional (3D) models of these four proteases were constructed with a comparative molecular modeling technique based on satisfaction of spatial constraints. The models were used to predict immunogenic epitopes and surface regions that are likely to interact with proteoglycans. Nine potential antigenic segments in the four chymases were identified on the basis of solvent accessibility, protrusion, flexibility, and sequence variability. These segments are suitable epitopes for preparation of protease-specific antipeptide immunoglobulin. Two regions with net charges ranging from +6 to +10 at neutral pH were found on the surfaces of mMCP-4 and mMCP-5. The two regions are located far from the substrate binding cleft at diametrically opposite ends of the folded proteases. A strong positive electrostatic potential surrounds the two regions. Thus, they are good candidates for binding sites that interact with heparin proteoglycan in the granules of serosal mast cells. In contrast, mMCP-1 and mMCP-2, which are present in granules of mucosal mast cells that contain chondroitin sulfate, lack one of these regions and have a lower charge density in the other. The differences between the 3D models provide a structural basis for the selective localization of specific chymases within mouse mast cells that contain different proteoglycans.

Amino Acid Sequence↗
PubMed1993

Percutaneous endoscopic gastrostomy: the Heidelberg Repatriation Hospital experience.

Percutaneous endoscopic gastrostomy (PEG) was performed on 32 patients (mean age 75 years) who were dysphagic but enteral alimentation was possible. Seventeen patients were recovering from a stroke; the interval between the onset of stroke and PEG averaged 44 days. The procedure was successful and well tolerated by 16 of these 17 patients. Ten patients (31%) still had a functioning PEG, a median of 30 weeks after placement. Seven patients whose swallowing recovered had their tubes removed an average of 3 months after their insertion. Fifteen patients (47%) subsequently died from their underlying disease, a mean of 126 days following PEG. There were no deaths directly related to catheter placement. Percutaneous endoscopic gastrostomy is a useful alternative to surgical gastrostomy in elderly patients with long-term oral feeding problems.

Adult↗
PubMed1993

Control engineering for planning drug therapy.

An optimal drug input may be defined as producing an ideal therapeutic effect as closely as possible without exceeding predetermined safety limits on any adverse drug effects. The intensity and time patterns of the drug-elicited response are functions of the pharmacodynamic properties of the drug in the patient. Drug input optimisation can be considered as a control problem and the different control engineering techniques may serve to assist in planning/implementing drug dosage regimens. This paper reviews some problems associated with planning optimal drug therapy in different clinical context and illustrates the solution of such problems by clinical examples.

Biomedical Engineering↗
PubMed1992

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.

The local environment of an amino acid in a folded protein determines the acceptability of mutations at that position. In order to characterize and quantify these structural constraints, we have made a comparative analysis of families of homologous proteins. Residues in each structure are classified according to amino acid type, secondary structure, accessibility of the side chain, and existence of hydrogen bonds from the side chains. Analysis of the pattern of observed substitutions as a function of local environment shows that there are distinct patterns, especially for buried polar residues. The substitution data tables are available on diskette with Protein Science. Given the fold of a protein, one is able to predict sequences compatible with the fold (profiles or templates) and potentially to discriminate between a correctly folded and misfolded protein. Conversely, analysis of residue variation across a family of aligned sequences in terms of substitution profiles can allow prediction of secondary structure or tertiary environment.

Amino Acid Sequence↗
PubMed1992

Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases.

We report the X-ray analysis at 2.0 A resolution for crystals of the aspartic proteinase endothiapepsin (EC 3.4.23.6) complexed with a potent difluorostatone-containing tripeptide renin inhibitor (CP-81,282). The scissile bond surrogate, an electrophilic ketone, is hydrated in the complex. The pro-(R) (statine-like) hydroxyl of the tetrahedral carbonyl hydrate is hydrogen-bonded to both active-site aspartates 32 and 215 in the position occupied by a water in the native enzyme. The second hydroxyl oxygen of the hydrate is hydrogen-bonded only to the outer oxygen of Asp 32. These experimental data provide a basis for a model of the tetrahedral intermediate in aspartic proteinase-mediated cleavage of the amide bond. This indicates a mechanism in which Asp 32 is the proton donor and Asp 215 carboxylate polarizes a bound water for nucleophilic attack. The mechanism involves a carboxylate (Asp 32) that is stabilized by extensive hydrogen bonding, rather than an oxyanion derivative of the peptide as in serine proteinase catalysis.

Amino Acid Sequence↗