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https://www.readbyqxmd.com/read/27914253/protein-conjugation-with-pamam-nanoparticles-microscopic-and-thermodynamic-analysis
#1
P Chanphai, E Froehlich, J S Mandeville, H A Tajmir-Riahi
PAMAM dendrimers form strong protein conjugates that are used in drug delivery systems. We report the thermodynamic and binding analysis of polyamidoamine (PAMAM-G4) conjugation with human serum albumin (HSA), bovine serum albumin (BSA) and milk beta-lactoglobulin (b-LG) in aqueous solution at physiological pH. Hydrophobicity played a major role in PAMAM-protein interactions with more hydrophobic b-LG forming stronger polymer-protein conjugates. Thermodynamic parameters showed PAMAM-protein bindings occur via hydrophobic and H-bonding contacts for b-LG, while van der waals and H-bonding interactions prevail in HSA and BSA-polymer conjugates...
November 27, 2016: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/27914116/so-it-is-so-it-shall-be-group-regularities-license-children-s-prescriptive-judgments
#2
Steven O Roberts, Susan A Gelman, Arnold K Ho
When do descriptive regularities (what characteristics individuals have) become prescriptive norms (what characteristics individuals should have)? We examined children's (4-13 years) and adults' use of group regularities to make prescriptive judgments, employing novel groups (Hibbles and Glerks) that engaged in morally neutral behaviors (e.g., eating different kinds of berries). Participants were introduced to conforming or non-conforming individuals (e.g., a Hibble who ate berries more typical of a Glerk)...
December 3, 2016: Cognitive Science
https://www.readbyqxmd.com/read/27914066/computational-tools-for-allosteric-drug-discovery-site-identification-and-focus-library-design
#3
Wenkang Huang, Ruth Nussinov, Jian Zhang
Allostery is an intrinsic phenomenon of biological macromolecules involving regulation and/or signal transduction induced by a ligand binding to an allosteric site distinct from a molecule's active site. Allosteric drugs are currently receiving increased attention in drug discovery because drugs that target allosteric sites can provide important advantages over the corresponding orthosteric drugs including specific subtype selectivity within receptor families. Consequently, targeting allosteric sites, instead of orthosteric sites, can reduce drug-related side effects and toxicity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914061/probing-oligomerized-conformations-of-defensin-in-the-membrane
#4
Wenxun Gan, Dina Schneidman, Ning Zhang, Buyong Ma, Ruth Nussinov
Computational prediction and design of membrane protein-protein interactions facilitate biomedical engineering and biotechnological applications. Due to their antimicrobial activity, human defensins play an important role in the innate immune system. Human defensins are attractive pharmaceutical targets due to their small size, broad activity spectrum, reduced immunogenicity, and resistance to proteolysis. Protein engineering based modification of defensins can improve their pharmaceutical properties. Here we present an approach to computationally probe defensins' oligomerization states in the membrane...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914060/a-protocol-for-the-design-of-protein-and-peptide-nanostructure-self-assemblies-exploiting-synthetic-amino-acids
#5
Nurit Haspel, Jie Zheng, Carlos Aleman, David Zanuy, Ruth Nussinov
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914056/parallel-computational-protein-design
#6
Yichao Zhou, Bruce R Donald, Jianyang Zeng
Computational structure-based protein design (CSPD) is an important problem in computational biology, which aims to design or improve a prescribed protein function based on a protein structure template. It provides a practical tool for real-world protein engineering applications. A popular CSPD method that guarantees to find the global minimum energy solution (GMEC) is to combine both dead-end elimination (DEE) and A* tree search algorithms. However, in this framework, the A* search algorithm can run in exponential time in the worst case, which may become the computation bottleneck of large-scale computational protein design process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914052/applications-of-normal-mode-analysis-methods-in-computational-protein-design
#7
Vincent Frappier, Matthieu Chartier, Rafael Najmanovich
Recent advances in coarse-grained normal mode analysis methods make possible the large-scale prediction of the effect of mutations on protein stability and dynamics as well as the generation of biologically relevant conformational ensembles. Given the interplay between flexibility and enzymatic activity, the combined analysis of stability and dynamics using the Elastic Network Contact Model (ENCoM) method has ample applications in protein engineering in industrial and medical applications such as in computational antibody design...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914050/multistate-computational-protein-design-with-backbone-ensembles
#8
James A Davey, Roberto A Chica
The ability of computational protein design (CPD) to identify protein sequences possessing desired characteristics in vast sequence spaces makes it a highly valuable tool in the protein engineering toolbox. CPD calculations are typically performed using a single-state design (SSD) approach in which amino-acid sequences are optimized on a single protein structure. Although SSD has been successfully applied to the design of numerous protein functions and folds, the approach can lead to the incorrect rejection of desirable sequences because of the combined use of a fixed protein backbone template and a set of rigid rotamers...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914047/deterministic-search-methods-for-computational-protein-design
#9
Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe
One main challenge in Computational Protein Design (CPD) lies in the exploration of the amino-acid sequence space, while considering, to some extent, side chain flexibility. The exorbitant size of the search space urges for the development of efficient exact deterministic search methods enabling identification of low-energy sequence-conformation models, corresponding either to the global minimum energy conformation (GMEC) or an ensemble of guaranteed near-optimal solutions. In contrast to stochastic local search methods that are not guaranteed to find the GMEC, exact deterministic approaches always identify the GMEC and prove its optimality in finite but exponential worst-case time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914044/the-framework-of-computational-protein-design
#10
Ilan Samish
Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo- (or other) stability to specific requested reactions such as protein-protein binding, enzymatic reactions, or nanotechnology applications. The design scheme may encompass small regions of the proteins or the entire protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914004/hybrid-receptor-bound-mm-gbsa-per-residue-energy-based-pharmacophore-modelling-enhanced-approach-for-identification-of-selective-lta4h-inhibitors-as-potential-anti-inflammatory-drugs
#11
Patrick Appiah-Kubi, Mahmoud Soliman
Leukotriene A4 hydrolase has been identified as an enzyme with dual anti- and pro-inflammatory role, thus, the conversion of leukotriene to leukotriene B4 in the initiation stage of inflammation and the removal of the chemotactic Pro-Gly-Pro tripeptide. These findings make leukotriene A4 hydrolase an attractive drug target: suggesting an innovative approach towards the identification and design of novel class of compounds that can selectively inhibit leukotriene B4 synthesis while sparing the aminopeptidase activity...
December 2, 2016: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/27913731/disentangling-polydispersity-in-the-pcna-p15paf-complex-a-disordered-transient-and-multivalent-macromolecular-assembly
#12
Tiago N Cordeiro, Po-Chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco J Blanco, Jochen S Hub, Ramon Crehuet, Pau Bernadó
The intrinsically disordered p15(PAF) regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15(PAF) and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913377/optimization-and-assessment-of-three-different-high-performance-liquid-chromatographic-systems-for-the-combinative-fingerprint-analysis-and-multi-ingredients-quantification-of-sangju-ganmao-tablet
#13
Meng-Zhe Guo, Jie Han, Dan-Dan He, Jia-Hui Zou, Zheng Li, Yan Du, Dao-Quan Tang
Chromatographic separation is still a critical subject for the quality control of traditional Chinese medicine. In this study, three different high performance liquid chromatographic (HPLC) systems employing commercially available columns packed with 1.8, 3.5 and 5.0 μm particles were respectively developed and optimized for the combinative fingerprint analysis and multi-ingredients quantification of Sangju Ganmao tablet (SGT). Chromatographic parameters including the repeatability of retention time and peak area, symmetry factor, resolution, number of theoretical plates and peak capacity were used to assess the chromatographic performance of different HPLC systems...
December 1, 2016: Journal of Chromatographic Science
https://www.readbyqxmd.com/read/27913358/conformational-sampling-of-a-biomolecular-rugged-energy-landscape
#14
Jakub Rydzewski, Rafal Jakubowski, Giuseppe Nicosia, Wieslaw Nowak
The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field...
December 1, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27913309/sequence-determinants-of-the-caenhorhabditis-elegansdopamine-transporter-dictating-in-vivoaxonal-export-and-synaptic-localization
#15
Sarah B Robinson, J Andrew Hardaway, Shannon L Hardie, Jane Wright, Ryan M Glynn, Daniel P Bermingham, Qiao Han, Sarah M Sturgeon, Phyllis Freeman, Randy D Blakely
The monoamine neurotransmitter dopamine (DA) acts across phylogeny to modulate both simple and complex behaviors. The presynaptic DA transporter (DAT) is a major determinant of DA signaling capacity in ensuring efficient extracellular DA clearance. In humans, DAT is also a major target for prescribed and abused psychostimulants. Multiple structural determinants of DAT function and regulation have been defined, though largely these findings have arisen from heterologous expression or ex vivo cell culture studies...
November 29, 2016: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/27913285/autosomal-recessive-spinocerebellar-ataxia-20-report-of-a-new-patient-and-review-of-literature
#16
Anju Shukla, Priyanka Upadhyai, Jhanvi Shah, K Neethukrishna, Stephanie Bielas, K M Girisha
Inherited ataxias are an extremely heterogeneous group of disorders. Autosomal recessive spinocerebellar ataxia 20 (SCAR20) is a recently described disorder characterized by intellectual disability, ataxia, coarse facial features, progressive loss of Purkinje cells in the cerebellum and often hearing loss and skeletal abnormalities. Mutations in the gene SNX14, which plays an important role in autophagy, have been found to cause SCAR20. The unique clinical findings of progressive coarsening of facial features makes the clinical phenotype recognizable among the various hereditary ataxias...
November 29, 2016: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/27913192/the-cellular-protein-nucleolin-preferentially-binds-long-looped-g-quadruplex-nucleic-acids
#17
Sara Lago, Elena Tosoni, Matteo Nadai, Manlio Palumbo, Sara N Richter
BACKGROUND: G-quadruplexes (G4s) are four-stranded nucleic acid structures that form in G-rich sequences. Nucleolin (NCL) is a cellular protein reported for its functions upon G4 recognition, such as induction of neurodegenerative diseases, tumor and virus mechanisms activation. We here aimed at defining NCL/G4 binding determinants. METHODS: Electrophoresis mobility shift assay was used to detect NCL/G4 binding; circular dichroism to assess G4 folding, topology and stability; dimethylsulfate footprinting to detect G bases involved in G4 folding...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27913116/multiple-conformations-of-gal3-protein-drive-the-galactose-induced-allosteric-activation-of-the-gal-genetic-switch-of-saccharomyces-cerevisiae
#18
Rajesh Kumar Kar, Hungyo Kharerin, Ranjith Padinhateeri, Paike Jayadeva Bhat
Gal3p is an allosteric monomeric protein which activates the GAL genetic switch of Saccharomyces cerevisiae in response to galactose. Expression of constitutive mutant of Gal3p or overexpression of wild-type Gal3p activates the GAL switch in the absence of galactose. These data suggest that Gal3p exists as an ensemble of active and inactive conformations. Structural data has indicated that Gal3p exists in open (inactive) and closed (active) conformations. However, mutant of Gal3p that predominantly exists in inactive conformation and yet capable of responding to galactose has not been isolated...
November 29, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27913058/effect-of-urea-on-protein-ligand-association
#19
Lora Stepanian, Ikbae Son, Tigran V Chalikian
We combine experimental and theoretical approaches to investigate the influence of a cosolvent on a ligand-protein association event. We apply fluorescence measurements to determining the affinity of the inhibitor tri-N-acetylglucosamine [(GlcNAc)3] for lysozyme at urea concentrations ranging from 0 to 8M. Notwithstanding that, at room temperature and neutral pH, lysozyme retains its native conformation up to the solubility limit of urea, the affinity of (GlcNAc)3 for the protein steadily decreases as the concentration of urea increases...
November 25, 2016: Biophysical Chemistry
https://www.readbyqxmd.com/read/27912177/raman-spectroscopy-and-quantum-mechanical-analysis-of-tautomeric-forms-in-cytosine-and-5-methylcytosine-on-gold-surfaces
#20
Dinh Bao Nguyen, Thanh Danh Nguyen, Sangsoo Kim, Sang-Woo Joo
Spectral differences between cytosine (Cyt) and 5-methylcytosine (5MC) were investigated by means of Raman spectroscopy with a combination of density functional theory (DFT) calculations. Surface-enhanced Raman scattering (SERS) revealed discriminating peaks of 5MC from those of Cyt upon adsorption on gold nanoparticles (AuNPs). Among the notable features, the multiple bands between 850 and 700cm(-1) for the ring-breathing modes of 5MC and Cyt could be correlated well with the simulated spectra based on the DFT calculations of the adsorbates on the gold cluster atoms...
November 9, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
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