Tableau-based protein substructure search using quadratic programming

Background  

Searching for proteins that contain similar substructures is an important task in structural biology. The exact solution of most formulations of this problem, including a recently published method based on tableaux, is too slow for practical use in scanning a large database.     

Validation of metabolic pathway databases based on chemical substructure search

Metabolic pathway databases such as KEGG contain information on thousands of biochemical reactions drawn from the biomedical literature. Ensuring consistency of such large metabolic pathways is essential to their proper use. In this paper, we present a new method to determine consistency of an important class of biochemical reactions. Our method exploits the knowledge of the atomic rearrangement pattern in biochemical reactions, to reduce the automatic atom mapping problem to a series of chemical substructure searches between the substrate and the product of a biochemical reaction. As an illustrative application, we describe the exhaustive validation of a substantial portion from the latest release of the KEGG LIGAND database.     

Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

Background  

Virtual screening methods are now well established as effective to identify hit and lead candidates and are fully integrated in most drug discovery programs. Ligand-based approaches make use of physico-chemical, structural and energetics properties of known active compounds to search large chemical libraries for related and novel chemotypes. While 2D-similarity search tools are known to be fast and efficient, the use of 3D-similarity search methods can be very valuable to many research projects as integration of 3D knowledge can facilitate the identification of not only related molecules but also of chemicals possessing distant scaffolds as compared to the query and therefore be more inclined to scaffolds hopping. To date, very few methods performing this task are easily available to the scientific community.     

Combining pharmacophore, docking and substructure search approaches to identify and optimize novel B-Raf(V600E) inhibitors

In this study for searching novel B-Raf(V600E) inhibitors, pharmacophore-based virtual screening identified 1 as a hit bearing 5-benzylidene-2-thioxodihydropyrimidine-4,6(1H,5H)-dione. Based on 1, scaffold hopping inspired by molecular docking discovered 5-(furan-2-ylmethylene)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione as a new and better scaffold. Substructure search with the new scaffold identified 28 active compounds, among which 12 compounds (42.9%) showed IC(50) less than 1μM. Especially, compound 3o, which is 10-fold more potent than the hit 1, is a potent inhibitor comparable to that of the marketed drug vemurafenib.     

Proteolytic substructure of brain myosin

Individual bovine brain myosin molecules visualized by electron microscopy consist of two globular heads and a fibrous tail, like myosin molecules from other sources. Brain myosin, however, showed much lower solubility at moderate to high ionic strength (0.2 to 0.4 M KCl) than gizzard myosin, and the filaments formed at low ionic strength in the presence of Mg2+ were fairly resistant to low concentrations of ATP, by which gizzard myosin filaments were completely solubilized. Brain myosin was digested with low concentrations of papain, alpha-chymotrypsin, or trypsin, and the fragmentation patterns were analyzed by means of polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, sedimentation at low ionic strength, and electron microscopy of the fragments produced. The results indicate that all of the proteases cleave the myosin molecule primarily at sites located in the neck or in the head close to the neck, suggesting that the brain myosin molecule contains a hinge region or an open peptide stretch around these sites. The differences as well as the similarities between the proteolytic fragmentation patterns of brain myosin and other myosins are discussed.     

Core substructure in cyanobacterial phycobilisomes

The tricylindrical core of Synechocystis 6701 phycobilisomes is made up of four types of allophycocyanin-containing complexes: A, (alpha AP beta AP)3; B, (alpha AP beta AP)3 .10K; C, (alpha APB1 alpha AP2 beta AP3).10K; D, (alpha AP beta AP)2.18.5K.99K; where AP is allophycocyanin, APB is allophycocyanin B, and 10K, 18.5K, and 99K are polypeptides of 10,000, 18,500, and 99,000 daltons, respectively. The 18.5K polypeptide is a hitherto unrecognized biliprotein subunit with a single phycocyanobilin prosthetic group. The tricylindrical core is made up of 12 subcomplexes in the molar ratio of A:B:C:D: of 4:4:2:2. Complexes C and D act as terminal energy acceptors. From these results and previous analysis of the bicylindrical core of Synechococcus 6301 phycobilisomes [14,15] it is proposed that the two cylinders of the Synechocystis 6701 core, proximal to the thylakoid membrane, each have the composition ABCD, and that the distal cylinder has the composition A2B2.     

LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value

Searching for protein structure-function relationships using three-dimensional (3D) structural coordinates represents a fundamental approach for determining the function of proteins with unknown functions. Since protein structure databases are rapidly growing in size, the development of a fast search method to find similar protein substructures by comparison of protein 3D structures is essential. In this article, we present a novel protein 3D structure search method to find all substructures with root mean square deviations (RMSDs) to the query structure that are lower than a given threshold value. Our new algorithm runs in O(m + N/m(0.5)) time, after O(N log N) preprocessing, where N is the database size and m is the query length. The new method is 1.8-41.6 times faster than the practically best known O(N) algorithm, according to computational experiments using a huge database (i.e., >20,000,000 C-alpha coordinates).     

Efficient substructure RMSD query algorithms.

Protein structure analysis is a very important research topic in the molecular biology of the post-genomic era. The root mean square deviation (RMSD) is the most frequently used measure for comparing two protein three-dimensional (3-D) structures. In this paper, we deal with two fundamental problems related to the RMSD. We first deal with a problem called the "range RMSD query" problem. Given an aligned pair of structures, the problem is to compute the RMSD between two aligned substructures of them without gaps. This problem has many applications in protein structure analysis. We propose a linear-time preprocessing algorithm that enables constant-time RMSD computation. Next, we consider a problem called the "substructure RMSD query" problem, which is a generalization of the above range RMSD query problem. It is a problem to compute the RMSD between any substructures of two unaligned structures without gaps. Based on the algorithm for the range RMSD problem, we propose an O(nm) preprocessing algorithm that enables constant-time RMSD computation, where n and m are the lengths of the given structures. Moreover, we propose O(nm log r/r)-time and O(nm/r)-space preprocessing algorithm that enables O(r) query, where r is an arbitrary integer such that 1 < or = r < or = min(n, m). We also show that our strategy also works for another measure called the unit-vector root mean square deviation (URMSD), which is a variant of the RMSD.     

The foldon substructure of staphylococcal nuclease

To search for submolecular foldon units, the spontaneous reversible unfolding and refolding of staphylococcal nuclease under native conditions was studied by a kinetic native-state hydrogen exchange (HX) method. As for other proteins, it appears that staphylococcal nuclease is designed as an assembly of well-integrated foldon units that may define steps in its folding pathway and may regulate some other functional properties. The HX results identify 34 amide hydrogens that exchange with solvent hydrogens under native conditions by way of large transient unfolding reactions. The HX data for each hydrogen measure the equilibrium stability (ΔG_HX) and the kinetic unfolding and refolding rates (k_op and k_cl) of the unfolding reaction that exposes it to exchange. These parameters separate the 34 identified residues into three distinct HX groupings. Two correspond to clearly defined structural units in the native protein, termed the blue and red foldons. The remaining HX grouping contains residues, not well separated by their HX parameters alone, that represent two other distinct structural units in the native protein, termed the green and yellow foldons. Among these four sets, a last unfolding foldon (blue) unfolds with a rate constant of 6 × 10^− 6 s^− 1 and free energy equal to the protein's global stability (10.0 kcal/mol). It represents part of the β-barrel, including mutually H-bonding residues in the β4 and β5 strands, a part of the β3 strand that H-bonds to β5, and residues at the N-terminus of the α2 helix that is capped by β5. A second foldon (green), which unfolds and refolds more rapidly and at slightly lower free energy, includes residues that define the rest of the native α2 helix and its C-terminal cap. A third foldon (yellow) defines the mutually H-bonded β1-β2-β3 meander, completing the native β-barrel, plus an adjacent part of the α1 helix. A final foldon (red) includes residues on remaining segments that are distant in sequence but nearly adjacent in the native protein. Although the structure of the partially unfolded forms closely mimics the native organization, four residues indicate the presence of some nonnative misfolding interactions. Because the unfolding parameters of many other residues are not determined, it seems likely that the concerted foldon units are more extensive than is shown by the 34 residues actually observed.     

Core substructure in Mastigocladus laminosus phycobilisomes

A native high molecular complex (M_r 850000) containing about 50% of the allphycocyanin of the phycobilisome but lacking allophycocyanin B was separated from isolated phycobilisomes by gel electrophoresis. It was designated AP_CM since the large linker polypeptide L_CM was exclusively localized in this complex. The complex exhibited a ?196°C fluorescence emission maximum at 673 nm (671 nm at 25°C). In addition, a core complex (designated AP_C, M_r≥1000000) consisting of both AP_CM and AP 680 was isolated by combined gel filtration and linear gradient centrifugation. At 25°C this complex showed dual emission peaks at 670 and 680 nm demonstrating functional independence of the terminal emitters. A complex similar to AP_CM can be isolated from phycobilisomes of Anabaena variabilis. This is evidence that AP_CM is the constitutive center of the tricylindrical core of hemidiscoidal cyanobacterial phycobilisomes. Two models summarizing the structural and functional consequences of the results are presented in the discussion.     

The protofilament substructure of amyloid fibrils

Tissue deposition of normally soluble proteins, or their fragments, as insoluble amyloid fibrils causes the usually fatal, acquired and hereditary systemic amyloidoses and is associated with the pathology of Alzheimer's disease, type 2 diabetes and the transmissible spongiform encephalopathies. Although each type of amyloidosis is characterised by a specific amyloid fibril protein, the deposits share pathognomonic histochemical properties and the structural morphology of all amyloid fibrils is very similar. We have previously demonstrated that transthyretin amyloid fibrils contain four constituent protofilaments packed in a square array. Here, we have used cross-correlation techniques to average electron microscopy images of multiple cross-sections in order to reconstruct the sub-structure of ex vivo amyloid fibrils composed of amyloid A protein, monoclonal immunoglobulin lambda light chain, Leu60Arg variant apolipoprotein AI, and Asp67His variant lysozyme, as well as synthetic fibrils derived from a ten-residue peptide corresponding to the A-strand of transthyretin. All the fibrils had an electron-lucent core but the packing arrangement comprised five or six protofilaments rather than four. The structural similarity that defines amyloid fibres thus exists principally at the level of beta-sheet folding of the polypeptides within the protofilament, while the different types vary in the supramolecular assembly of their protofilaments.     

The LabelHash algorithm for substructure matching

Background  

There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. However, experimental protein function determination is expensive and very time-consuming. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity.     

Core substructure in Mastigocladus laminosus phycobilisomes

Three allophycocyanin complexes were separated by gel electrophoresis, isoelectric focusing and ion exchange chromatography from a low molecular fraction (M_r 100–150000) of partially dissociated phycobilisomes of Mastigocladus laminosus: A. (^APAP); B. (^*AP₂ ^AP₂ ^AP*AP) · L _C ¹⁰ ; and C. (^*APAPBAP₂ ^AP*AP) · L _C ¹⁰ . According to their fluorescence emission maximum at room temperature the complexes A., B. and C. are designated AP 660, AP 664 and AP 680. The different subunits of the AP complexes have apparent molecular weights of M_r 18500 ^*AP, 18200 ^APB, 18000 ^AP, 17000 ^AP and 16500 ^*AP. This hitherto unrecognized microheterogeneity within the AP subunits of complexes B. and C. of Mastigocladus laminosus phycobilisomes could also be demonstrated and confirmed with the two phycocyanin complexes PC 642 and PC 646. PC 642 is characterized by a L _R ¹¹ linker polypeptide.Abbreviations AP allophycocyanin - PC phycocyanin - PEC phycoerythrocyanin - PE phycoerythrin - PAGE polyacrylamide gel electrophoresis - IEF isoelectric focusing - pI isoelectric point - M_r apparent molecular weight - TMED tetramethylethylenediamine - APS ammonium persulphate - SDS sodium dodecylsulphate - O.D. optical density A preliminary account of this work has been presented at the Embo Workshop on Oxygenic and Anoxygenic Electron Transport Systems in Cyanobacteria (Blue-green Algae) in Cape Sounion, Greece, 20–25 September 1987