A computer program for the design of optimal synthetic oligonucleotide probes for protein coding genes

A computer program has been written in FORTRAN 77 to locateon a protein sequence a region with optimum length and limiteddegeneracy in order to design artificial oligonucleotide probesfor use in molecular cloning. In addition the program checksfor regions of homology between this probe and any other basesequence found in nucleotide sequence data banks. There areoptions in the program to eliminate rare codons or to make preferentialchoices of bases in order to minimize the degeneracy of probes. Received on February 17, 1987; accepted on June 26, 1987     

A generic protein purification method for protein complex characterization and proteome exploration.

We have developed a generic procedure to purify proteins expressed at their natural level under native conditions using a novel tandem affinity purification (TAP) tag. The TAP tag allows the rapid purification of complexes from a relatively small number of cells without prior knowledge of the complex composition, activity, or function. Combined with mass spectrometry, the TAP strategy allows for the identification of proteins interacting with a given target protein. The TAP method has been tested in yeast but should be applicable to other cells or organisms.     

A multiple alignment program for protein sequences

A program for the multiple alignment of protein sequences ispresented. The program is an extension of the fast alignmentprogram by Wilbur et al. (1984) into higher dimensions. Theuse of hash procedures on fragments of the protein sequencesincreases the speed of calculation. Thereby we also take intoaccount fragments which are present in some, but not in all,sequences considered. The results of some multiple alignmentsare given. Received on September 11, 1986; accepted on March 18, 1987     

Alpha-synuclein multistate folding thermodynamics: implications for protein misfolding and aggregation

Alpha-synuclein aggregation has been tightly linked with the pathogenesis of Parkinson's disease and other neurodegenerative disorders. Despite the protein's putative function in presynaptic vesicle regulation, the roles of lipid binding in modulating alpha-synuclein conformations and the aggregation process remain to be fully understood. This study focuses on a detailed thermodynamic characterization of monomeric alpha-synuclein folding in the presence of SDS, a well-studied lipid mimetic. Far-UV CD spectroscopy was employed for detection of conformational transitions induced by SDS, temperature, and pH. The data we present here clearly demonstrate the multistate nature of alpha-synuclein folding, which involves two predominantly alpha-helical partially folded thermodynamic intermediates that we designate as F (most folded) and I (intermediately folded) states. Likely structures of these alpha-synuclein conformational states are also discussed. These partially folded forms can exist in the presence of either monomeric or micellar forms of SDS, which suggests that alpha-synuclein has an intrinsic propensity for adopting multiple alpha-helical structures even in the absence of micelle or membrane binding, a feature that may have implications for its biological activity and toxicity. Additionally, we discuss the relation between alpha-synuclein three-state folding and its aggregation, within the context of isothermal titration calorimetry and transmission electron microscopy measurements of SDS-initiated oligomer formation.     

A fast and efficient program for modeling protein loops

We developed an efficient Monte Carlo Simulated Annealing (MCSA) program for modeling protein loops with high speed. The total conformational energy in each step of MCSA simulation consists of two parts: the nonbonded atomic interaction represented by a simple soft-sphere potential and the harmonic distance constraint to ensure the smooth connection of the loop segment to the rest of the protein structure. The soft-sphere potential was a simplified potential that has been successfully used by the authors in modeling the carbohydrate part of glycoprotein systems [H. Zhang, Y. Yang, L. Lai, and Y. Tang (1996), Carbohydrate Research, Vol. 284, pp. 25–34]. It only considers the purely repulsive steric interactions to avoid artificial attractive forces between atoms in the absence of solvent molecules. The N-terminal of the loop segment was connected to the bulk protein part, and two dummy main-chain atoms N and Cα immediately following the C-terminal of the loop segment were constrained to their real positions in the protein structure, which not only assures the correct geometry of loop-protein connection but also is more rigorous than the previous work. To improve the speed, two strategies, the local region method and grid-mapping method, were devised to accelerate the computation of environmental interaction that is responsible for the major part of the computing consumption. The grid-mapping method can reduce computational time dramatically. Conformations with rational steric packing and smooth connection to the rest of the protein structure were generated by the MCSA program, and then were refined by the empirical force field CHARMm [B. R. Brook, R. E. Braccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus (1983), Journal of Computational Chemistry, Vol. 4, pp. 187–217]. Bovine pancreatic trypsin inhibitor (BPTI) was used as an example to test the ability of loop modeling of the method, and five loops in BPTI were calculated. Conformations close to the crystal structure were generated for all of them. With the criteria of CHARMm energy, near-native conformations can be selected, for example, the backbone rms deviation 0.93 A from the crystal structure was gotten for the longest 9-residue loop. © 1997 John Wiley & Sons, Inc.     

A computer graphics program system for protein structure representation

We have developed a computer graphics program system for the schematic representation of several protein secondary structure analysis algorithms. The programs calculate the probability of occurrence of alpha-helix, beta-sheet and beta-turns by the method of Chou and Fasman and assign unique predicted structure to each residue using a novel conflict resolution algorithm based on maximum likelihood. A detailed structure map containing secondary structure, hydrophobicity, sequence identity, sequence numbering and the location of putative N-linked glycosylation sites is then produced. In addition, helical wheel diagrams and hydrophobic moment calculations can be performed to further analyze the properties of selected regions of the sequence. As they require only structure specification as input, the graphics programs can easily be adapted for use with other secondary structure prediction schemes. The use of these programs to analyze protein structure-function relationships is described and evaluated.     

A multistate Markov chain model for evaluating a sterilization policy

"A multistate Markov chain model corresponding to varying fertility and mortality rates at different levels of surviving children of a couple was developed. Asymptotic probabilities of having a fixed number of children have been worked out." The implied geographical focus is on India.     

A generic high-throughput screening assay for kinases: protein kinase a as an example

A generic high-throughput screening assay based on the scintillation proximity assay technology has been developed for protein kinases. In this assay, the biotinylated (33)P-peptide product is captured onto polylysine Ysi bead via avidin. The scintillation signal measuring the product formation increases linearly with avidin concentration due to effective capture of the product on the bead surface via strong coulombic interactions. This novel assay has been optimized and validated in 384-well microplates. In a pilot screen, a signal-to-noise ratio of 5- to 9-fold and a Z' factor ranging from 0.6 to 0.8 were observed, demonstrating the suitability of this assay for high-throughput screening of random chemical libraries for kinase inhibitors.     

A computer program for translating DNA sequences into protein.

This paper describes a comprehensive program for translating one or two DNA sequences into amino acid sequences. Written in FORTRAN, it was designed for maximum flexibility of use and easy maintenance, modification and portability. It has full comments throughout.     

MATRAS: A program for protein 3D structure comparison

The recent accumulation of large amounts of 3D structural data warrants a sensitive and automatic method to compare and classify these structures. We developed a web server for comparing protein 3D structures using the program Matras (http://biunit.aist-nara.ac.jp/matras). An advantage of Matras is its structure similarity score, which is defined as the log-odds of the probabilities, similar to Dayhoff's substitution model of amino acids. This score is designed to detect evolutionarily related (homologous) structural similarities. Our web server has three main services. The first one is a pairwise 3D alignment, which is simply align two structures. A user can assign structures by either inputting PDB codes or by uploading PDB format files in the local machine. The second service is a multiple 3D alignment, which compares several protein structures. This program employs the progressive alignment algorithm, in which pairwise 3D alignments are assembled in the proper order. The third service is a 3D library search, which compares one query structure against a large number of library structures. We hope this server provides useful tools for insights into protein 3D structures.     

A generic rate law for surface-active enzymes

Many biochemical reactions are confined to interfaces, such as membranes or cell walls. Despite their importance, no canonical rate laws describing the kinetics of surface-active enzymes exist. Combining the approach chosen by Michaelis and Menten 100 years ago with concepts from surface chemical physics, we here present an approach to derive generic rate laws of enzymatic processes at surfaces. We illustrate this by a simple reversible conversion on a surface to stress key differences to the classical case in solution. The available area function, a concept from surface physics which enters the rate law, covers different models of adsorption and presents a unifying perspective on saturation effects and competition between enzymes. A remarkable implication is the direct dependence of the rate of a given enzyme on all other enzymatic species able to bind at the surface. The generic approach highlights general principles of the kinetics of surface-active enzymes and allows to build consistent mathematical models of more complex pathways involving reactions at interfaces.     

Olga--oligonucleotide primer design program for the Atari ST

A program to facilitate the design of oligonucleotide primnershas been devised. Olga is written in draft ANSI standard ‘C’and makes use of the implementation of Digital Research GEM(Graphics Environment Manager) on the Atari ST Olga is specificallysuited to the polymnerase chain reaction (PCR) allowing si analysisof two primer sequences. The advantage of Olga is that it providesin one program analyses for direct repeats, secondary structuresand primer dimerization as well as several useful ‘finishing’tools for workers engaged in PCR optimization and oligonucleotidesyntheses.     

A media design program for lactic acid production coupled with extraction by electrodialysis

The aim of this study was to investigate industrial media for lactic acid fermentation to reduce the cost of nitrogen sources. Corn steep liquor (CSL) was successfully used at 5% (v/v) in batch fermentations. Use of soluble CSL improved the productivity approximately 20% with an advantage of clearer fermentation broth. Yeast extract (YE)-complemented CSL media further increased the productivity. It was found that 3.1 g L(-1) yeast extract and 5% CSL could be an effective substitute for 15 g L(-1) yeast extract in 10% glucose medium. Spent brewery yeast was also used as a sole nitrogen source equivalent to 5% CSL. Lactic acid was recovered by electrodialysis from the cell free broth. Depleted cell free broth supplemented with 5 g L(-1) of yeast extract performed reasonably in batch cultures. Reuse of the fermentation broth may reduce the cost of raw materials as well as minimize the fermentation wastes.     

A generic motif discovery algorithm for sequential data

MOTIVATION: Motif discovery in sequential data is a problem of great interest and with many applications. However, previous methods have been unable to combine exhaustive search with complex motif representations and are each typically only applicable to a certain class of problems. RESULTS: Here we present a generic motif discovery algorithm (Gemoda) for sequential data. Gemoda can be applied to any dataset with a sequential character, including both categorical and real-valued data. As we show, Gemoda deterministically discovers motifs that are maximal in composition and length. As well, the algorithm allows any choice of similarity metric for finding motifs. Finally, Gemoda's output motifs are representation-agnostic: they can be represented using regular expressions, position weight matrices or any number of other models for any type of sequential data. We demonstrate a number of applications of the algorithm, including the discovery of motifs in amino acids sequences, a new solution to the (l,d)-motif problem in DNA sequences and the discovery of conserved protein substructures. AVAILABILITY: Gemoda is freely available at http://web.mit.edu/bamel/gemoda     

A generic mechanism for adaptive growth rate regulation

How can a microorganism adapt to a variety of environmental conditions despite the existence of a limited number of signal transduction mechanisms? We show that for any growing cells whose gene expression fluctuate stochastically, the adaptive cellular state is inevitably selected by noise, even without a specific signal transduction network for it. In general, changes in protein concentration in a cell are given by its synthesis minus dilution and degradation, both of which are proportional to the rate of cell growth. In an adaptive state with a higher growth speed, both terms are large and balanced. Under the presence of noise in gene expression, the adaptive state is less affected by stochasticity since both the synthesis and dilution terms are large, while for a nonadaptive state both the terms are smaller so that cells are easily kicked out of the original state by noise. Hence, escape time from a cellular state and the cellular growth rate are negatively correlated. This leads to a selection of adaptive states with higher growth rates, and model simulations confirm this selection to take place in general. The results suggest a general form of adaptation that has never been brought to light—a process that requires no specific mechanisms for sensory adaptation. The present scheme may help explain a wide range of cellular adaptive responses including the metabolic flux optimization for maximal cell growth.     

A generic algorithm for layout of biological networks

Background  

Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.     

A generic rate equation for catalysed,template-directed polymerisation

Biosynthetic networks link to growth and reproduction processes through template-directed synthesis of macromolecules such as polynucleotides and polypeptides. No rate equation exists that captures this link in a way that it can effectively be incorporated into a single computational model of the overall process. This paper describes the derivation of such a generic steady-state rate equation for catalysed, template-directed polymerisation reactions with varying monomer stoichiometry and varying chain length. The derivation is based on a classical Michaelis–Menten mechanism with template binding and an arbitrary number of chain elongation steps that produce a polymer composed of an arbitrary number of monomer types. The rate equation only requires the identity of the first dimer in the polymer sequence; for the remainder only the monomer composition needs be known. Further simplification of a term in the denominator yielded an equation requiring no positional information at all, only the monomer composition of the polymer; this equation still gave an excellent estimate of the reaction rate provided that either the monomer concentrations are at least half-saturating, or the polymer is very long.     

HCABAND: A computer program for the 2D-helical representation of protein sequences

A BASIC program, HCABAND, is described which is used to convertthe linear amino acid sequence of proteins into a word processor-readablefile to generate the 2D-helical representation required forhydrophobic cluster analysis. The user can specify the widthof the plot and can use the word processor macro-commands tofacilitate visual inspection of the plots. The plots can beeasily stored on diskettes, mixed with text and printed. HCABANDfeatures are generally applicable and can be implemented onvirtually any microcomputer. Received on May 9, 1989; accepted on August 28, 1989