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Sippl, Charles J.

doi:10.1007/978-1-349-17843-8_13

Cited by 6 publications

(6 citation statements)

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“…Known structures are essential for comparative modeling and fold recognition. The secondary structure prediction techniques [32] are trained on libraries of known structures and many techniques that build structures from scratch either employ structural fragments derived from known folds [33,34] or employ knowledge based energy functions derived from the protein structure database [35^37]. Of course, the study and simulation of protein^ligand [38] and protein^protein interactions [39], and virtual screening depend on structures obtained from experiments.…”

Section: Resultsmentioning

confidence: 99%

The Role of Protein Structure in Genomics

Domingues¹,

Koppensteiner²,

Sippl³

2000

Biochemical Society Transactions

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MicroArrays of Gel Immobilized Compounds on a Chip (MAGIChipsTM)are produced by immobilizing oligonucleotides, DNA, enzymes, antibodies, and other compounds on a photopolymerized micromatrix of polyacrylamide gel pads 1OOX1OOX20 pm and smaller in size. Alternatively, allyl-modified compounds can be embedded within polyacrylamide gel pads by copolymerization. MAGIChips have been shown to be efficient for analysis of nucleic acid hybridization, specific binding of DNA with proteins, and low-molecular-weight compounds, and proteinprotein interactions. The three-dimensional gel pads of the microarrays can be used as nanoliter-sized microtest tubes to perform ligation, singlebase extension, PCR amplification of DNA, and other reactions. The fluorescence microscope has been devised for analyzing reactions on MAGIChips, including quantitative and real-time monitoring of hybridization, measuring the thermodynamic parameters of DNA duplexes containing different modified nucleotides, and measuring the kinetics of enzymatic reaction. On-chip MALDI-TOF mass spectrometry was successfully tested for analysis of DNA and protein interactions. Application of these biochips for detection of human polymorphism and mutations, identification of microorganisms and their drug resistant and toxin-bearing strains, and in different fields of biotechnology and medicine will be described.

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Section: Resultsmentioning

confidence: 99%

The Role of Protein Structure in Genomics

Domingues¹,

Koppensteiner²,

Sippl³

2000

Biochemical Society Transactions

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“…It is also interesting to compare the conformation of thymosin p4 derived from the NMR experiment with that predicted by the method of knowledge-based mean fields derived from a data base of known protein structures (Sippl et al, 1992). This procedure calculated the thymosin structure to be very close to the NMR structure of thymosin in the alcoholic solution and not to that of thymosin p4 in pure water (Sippl et al, 1992). A similar result to that obtained in alcohol solution is found for thymosin p4 by Garnier-Osguthorpe-Robson secondary-structure prediction (Voelter, 1992).…”

Section: Discussionmentioning

confidence: 99%

Conformation of thymosin β₄ in water determined by NMR spectroscopy

Czisch

Schleicher

Hörger

et al. 1993

European Journal of Biochemistry

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The conformational preferences of a 43-amino-acid G-actin-binding peptide, thymosin P4, in water at 1, 4 and 14°C and at pH 3.0 and 6.5 were studied by NMR. NMR showed that thymosin p4 lacks a uniquely folded conformation in water. However, some preferential a-helical conformations of thymosin /I4 can be observed in aqueous solutions. The segment at residues 5-16 showed characteristic interactions for conformations in both the P-strand and a-helical regions of the 4-y space, based on strong CH(i)-NH(i+ 1) interactions and NH-NH, C"H(i)-NH(i+3), and C"H(i)-CpH(i+3) interactions, respectively. At 1 -4"C, another segment at residues 31 -37 also shows both p and a conformations, forming however a less well-defined helix than the segment at residues 5 -16. At 14"C, the conformational population of the helix at positions 5-16 is shifted more towards the random and turn-like structures, whereas the segment at positions 31 -37 becomes exclusively a random coil.The cytoplasmic salt conditions in a non-muscle cell strongly favor the polymerization of actin and only recently has it been determined how cells manage to keep more than 50% of the actin pool in an unpolymerized state. It is now thought that thymosin P4 is the main actin-sequestering peptide, which forms a 1 : 1 complex with actin and thus shifts the polymerization equilibrium from filamentous (F-actin) to globular actin (G-actin;Weeds and Way, 1991;Safer, 1992). Furthermore, the interaction of thymosin and actin inhibits of ADP/ATP exchange in actin, consequently leading to a high concentration of ADP-actin, which has a drastically decreased tendency to form actin filaments. Profilins, another class of G-actin-binding proteins, increase the nucleotide exchange and are thought to compete with thymosin in this reaction (Goldschmidt-Clermont et al., 1992).Since the elucidation of the crystal structure of actin (Kabsch et al., 1990), it is of prime importance to determine the structures of actin-binding proteins and to characterize the nature of the protein/protein interactions. Recently, we determined the NMR structure of hisactophilin, a histidinerich actin-binding protein (Scheel et al., 1989;Habazettl et al., 1992), and of thymosin p4 (Zarbock et al., 1990). The latter, however, was obtained in solutions containing fluorinated alcohols, i.e. conditions which might not reflect the true conformation of the protein in the aqueous environment. We present in this study the determination of the solution conformation of thymosin / I 4 in water by 'H-NMR spectroscopy. Using a variety of two-dimensional (2D) NMR techniques (Emst et al., 1987), the 'H-NMR spectra were assigned in a sequential manner (Wuthrich, 1986 spectra formed the basis for the determination of the conformational preferences of thymosin p4 at different temperatures and pH. MATERIALS AND METHODS Sample preparation of thymosin p4Thymosin P4 was isolated as described by Zarbock et al. (1990). The NMR samples of thymosin P4 were dissolved in 90% H,0/10% D,O at an approximate concentration of 2 mM peptide...

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“…An energy function was developed for coarse-grained molecular simulation that accommodates chemical interference using Boltzmann inversion 37,42,43 from the data derived from all-atomistic molecular dynamics simulations. The pair correlation function between any two amino acid types i and j at a distance r in solvent type α is ) (r g ij α .…”

Section: Boltzmann Inversionmentioning

confidence: 99%

Multiscale investigation of chemical interference in proteins

Samiotakis

Homouz²,

Cheung

2010

The Journal of Chemical Physics

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We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in better exploring the energy landscape of a small protein under chemical interference such as chemical denaturation. An excessive amount of water molecules in all-atomistic molecular dynamics simulations often negatively impacts the sampling efficiency of some advanced sampling techniques such as the replica exchange method and it makes the investigation of chemical interferences on protein dynamics difficult. Thus, there is a need to develop an effective strategy that focuses on sampling structural changes in protein conformations rather than solvent molecule fluctuations. In this work, we address this issue by devising a multiscale simulation scheme (MultiSCAAL) that bridges the gap between all-atomistic molecular dynamics simulation and coarse-grained molecular simulation. The two key features of this scheme are the Boltzmann inversion and a protein atomistic reconstruction method we previously developed (SCAAL). Using MultiSCAAL, we were able to enhance the sampling efficiency of proteins solvated by explicit water molecules. Our method has been tested on the folding energy landscape of a small protein Trp-cage with explicit solvent under 8M urea using both the all-atomistic replica exchange molecular dynamics and MultiSCAAL. We compared computational analyses on ensemble conformations of Trp-cage with its available experimental NOE distances. The analysis demonstrated that conformations explored by MultiSCAAL better agree with the ones probed in the experiments because it can effectively capture the changes in side-chain orientations that can flip out of the hydrophobic pocket in the presence of urea and water molecules. In this regard, MultiSCAAL is a promising and effective sampling scheme for investigating chemical interference which presents a great challenge when modeling protein interactions in vivo.

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Cited by 6 publications

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The Role of Protein Structure in Genomics

The Role of Protein Structure in Genomics

Conformation of thymosin β₄ in water determined by NMR spectroscopy

Multiscale investigation of chemical interference in proteins

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M

Cited by 6 publications

References 0 publications

The Role of Protein Structure in Genomics

The Role of Protein Structure in Genomics

Conformation of thymosin β4 in water determined by NMR spectroscopy

Multiscale investigation of chemical interference in proteins

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Conformation of thymosin β₄ in water determined by NMR spectroscopy