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Side Chain

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Md Shariful Islam Bhuyan - One of the best experts on this subject based on the ideXlab platform.

  • A protein-dependent Side-Chain rotamer library
    BMC Bioinformatics, 2011
    Co-Authors: Md Shariful Islam Bhuyan

    Background Protein Side-Chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein Side-Chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, Side-Chain conformations are determined by spatially local information, rather than sequentially local information. Since in the Side-Chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. Methods In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Results Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the Side-Chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the Side-Chain prediction power of the protein-dependent library is still comparable to the global-search-based Side-Chain prediction methods.

Marcus Weck - One of the best experts on this subject based on the ideXlab platform.

  • non covalent Side Chain polymers design principles functionalization strategies and perspectives
    Chemical Society Reviews, 2005
    Co-Authors: Joel M Pollino, Marcus Weck

    Side-Chain functionalized polymers have a profound impact on complex materials synthesis with a variety of applications ranging from liquid crystalline and electro-optical materials to drug delivery systems. In the last decade, the use of self-assembly towards the synthesis of Side-Chain functionalized polymers has been investigated extensively as a result of its modular character and ease of synthesis. This tutorial review describes recent advances in the literature and establishes basic design principles and synthetic approaches towards the fabrication of supramolecular materials that are based on Side-Chain functionalized polymers.

Tobias Weidner - One of the best experts on this subject based on the ideXlab platform.

  • lk peptide Side Chain dynamics at interfaces are independent of secondary structure
    Physical Chemistry Chemical Physics, 2017
    Co-Authors: Michael A Donovan, Yeneneh Yimer, Helmut Lutz, Jim Pfaendtner, Mischa Bonn, Tobias Weidner

    Protein Side Chain dynamics are critical for specific protein binding to surfaces and protein-driven surface manipulation. At the same time, it is highly challenging to probe Side Chain motions specifically at interfaces. One important open question is the degree to which the motions of Side Chains are dictated by local protein folding or by interactions with the surface. Here, we present a real-time measurement of the orientational dynamics of leucine Side Chains within leucine–lysine (LK) model peptides at the water–air interface, with three representative peptide folds: α-helix, 310-helix and β-strand. The results, modeled and supported by molecular dynamics simulations, show that the different peptide folds exhibit remarkably similar sub-picosecond orientational Side Chain dynamics at the air/water interface. This demonstrates that the Side Chain motional dynamics is decoupled from the local secondary structure.

Yongfang Li - One of the best experts on this subject based on the ideXlab platform.

  • Side Chain engineering of high efficiency conjugated polymer photovoltaic materials
    Science China-chemistry, 2015
    Co-Authors: Zhi-guo Zhang, Yongfang Li

    In recent years, conjugated polymers have attracted great attention in the application as photovoltaic donor materials in polymer solar cells (PSCs). Broad absorption, lower-energy bandgap, higher hole mobility, relatively lower HOMO energy levels, and higher solubility are important for the conjugated polymer donor materials to achieve high photovoltaic performance. Side-Chain engineering plays a very important role in optimizing the physicochemical properties of the conjugated polymers. In this article, we review recent progress on the Side-Chain engineering of conjugated polymer donor materials, including the optimization of flexible Side-Chains for balancing solubility and intermolecular packing (aggregation), electron-withdrawing substituents for lowering HOMO energy levels, and two-dimension (2D)-conjugated polymers with conjugated Side-Chains for broadening absorption and enhancing hole mobility. After the molecular structural optimization by Side-Chain engineering, the 2D-conjugated polymers based on benzodithiophene units demonstrated the best photovoltaic performance, with power- conversion efficiency higher than 9%.

  • Side Chain Engineering of Polythiophene Derivatives with a Thienylene–Vinylene Conjugated Side Chain for Application in Polymer Solar Cells
    Macromolecules, 2012
    Co-Authors: Zhi-guo Zhang, Siyuan Zhang, Hua Geng, Zhigang Shuai, Yongfang Li

    Two new conjugated Side-Chain isolated polythiophene derivatives, PT4TV and PT4TV-C, were designed and synthesized by copolymerization of thiophene unit with thienylene–vinylene (TV) conjugated Side Chain and unsubstituted terthiophene unit. The difference of the two polymers is an additional carbonyl group on the conjugated TV Side Chain in PT4TV-C. Compared to previous reported conjugated Side Chain polythiophenes (CSC-PTs) with concentrated Side Chains, PT4TV and PT4TV–C showed red-shifted and enhanced π–π* transition absorption of the polymer backbone along with the shoulder peak and steep absorption edge, indicating ordered polymer main Chains and well-packed Side Chains. PT4TV possessed an absorption edge of 663 nm and a HOMO energy level at −5.21 eV. The introducing of electron deficient carbonyl group in PT4TV–C led to 17 nm red-shifted absorption and a down-shifted HOMO energy level at −5.26 eV, but aroused the issue of poorer planarity of the polymer backbone. The more ordered structure in PT4TV...

  • Effect of SideChain end groups on the optical, electrochemical, and photovoltaic properties of SideChain conjugated polythiophenes
    Journal of Polymer Science Part A, 2006
    Co-Authors: Erjun Zhou, Chang He, Chunhe Yang, Yongfang Li

    Three new Side-Chain conjugated polythiophene derivatives, poly{3-[2-(3-methoxy-4-octyloxy-phenyl)-vinyl]-thiophene} (P3MOPVT), poly{3-[2-(3,5-dimethoxy-4-octyloxy-phenyl)-vinyl]-thiophene} (P3DMOPVT), and poly{3-[2-(3,4-dioctyloxy-phenyl)-vinyl]-thiophene} (P3DOPVT), were synthesized by Wittig-Hornor reaction and GRIM method and compared with poly{3-[2-(4-octyloxy-phenyl)-vinyl]-thiophene} (P3OPVT) for investigating the effect of the end groups of the conjugated Side-Chain on the properties of the polymers. Owing to the electron-donating ability of methoxy groups, the visible absorption peaks of P3MOPVT and P3DMOPVT solutions and films become stronger and red-shifted compared with P3OPVT. The electrochemical bandgaps of the four polymers are 2.15 eV for P3OPVT, 1.99 eV for P3MOPVT, 1.85 eV for P3DMOPVT, and 2.36 eV for P3DOPVT, respectively, which indicate that the electron-donating ability of the methoxy end group on the conjugated Side Chain of P3MOPVT and P3DMOPVT and the large steric hindrance of the two octyloxy end groups on the conjugated Side Chain of P3DOPVT have obvious influence on the electrochemical properties of the Side-Chain conjugated polythiophenes. Polymer solar cells were fabricated with a structure of ITO/PEDOT:PSS/Polymer:PCBM/LiF/Al. The best device, based on P3DMOPVT, shows a power conversion efficiency of 1.63% under the illumination of AM1.5, 80 mW/cm2. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 4916–4922, 2006

Martin Karplus - One of the best experts on this subject based on the ideXlab platform.

  • backbone dependent rotamer library for proteins application to Side Chain prediction
    Journal of Molecular Biology, 1993
    Co-Authors: Roland L Dunbrack, Martin Karplus

    Abstract A backbone-dependent rotamer library for amino acid Side-Chains is developed and used for constructing protein Side-Chain conformations from the main-Chain co-ordinates. The rotamer library is obtained from 132 protein Chains in the Brookhaven Protein Database. A grid of 20° by 20° blocks for the main-Chain angles φ,ψ is used in the rotamer library. Significant correlations are found between Side-Chain dihedral angle probabilities and backbone φ,ψ values. These probabilities are used to place the Side-Chain on the known backbone in the test application for six proteins for which high-resolution crystal structures are available. A minimization scheme is used to reorient Side-Chains that conflict with the backbone or other Side-Chains after the initial placement. The initial placement yields 59% of both χ1 and χ2 values in the correct position (to within 40°) for thermolysin to 81% for crambin. After refinement the values range from 61% (lysozyme) to 89% (crambin). It is evident from the results that a single protein does not adequately test a prediction scheme. The computation time required by the method scales linearly with the number of Side-Chains. An initial prediction from the library takes only a few seconds of computer time, while the iterative refinement takes on the order of hours. The method is automated and can easily be applied to aid experimental Side-Chain determinations and homology modeling. The high degree of correlation between backbone and Side-Chain conformations may introduce a simplification in the protein folding process by reducing the available conformational space.