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Chemie der Biomakromolekuele


 
Aktuelle Fachartikel zur Chemie von biologischen Makromolekuelen, sortiert nach Erscheinungsdatum.

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Auf dieser Seite beruecksichtige naturwissenschaftliche Journale:


BMC Structural Biology - published by BioMed Central -
... is an open access journal publishing original peer-reviewed research articles in investigations into the structure and function of biological macromolecules.

Biomacromolecules - published by The American Chemical Society -
... explores the interactions of macromolecules with biological systems and their environments as well as biological approaches to the design of polymeric materials. Cutting-edge research at the interface of polymer science and biological sciences.



Aktuelle wissenschaftliche Fachartikel der genannten Journale:


Monolayer Film Behavior of Lipopolysaccharide from Pseudomonas aeruginosa at the Air−Water Interface

Thomas Abraham, Sarah R. Schooling, Terry J. Beveridge, and John Katsaras
Web Release Date: Sat, 6 Sep 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800562r

Quelle: Biomacromolecules | 6 Sep 2008 | 6:00 am CEST

Synthesis of Cellulose-graft-Poly(N,N-dimethylamino-2-ethyl methacrylate) Copolymers via Homogeneous ATRP and Their Aggregates in Aqueous Media

Xiaofeng Sui, Jinying Yuan, Mi Zhou, Jun Zhang, Haijun Yang, Weizhong Yuan, Yen Wei, and Caiyuan Pan
Web Release Date: Sat, 6 Sep 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800538d

Quelle: Biomacromolecules | 6 Sep 2008 | 6:00 am CEST

Functionalized Polycarbonate Derived from Tartaric Acid: Enzymatic Ring-Opening Polymerization of a Seven-Membered Cyclic Carbonate

Ruizhi Wu, Talal F. Al-Azemi, and Kirpal S. Bisht
Web Release Date: Fri, 5 Sep 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800696q

Quelle: Biomacromolecules | 5 Sep 2008 | 6:00 am CEST

Synthesis and Antimicrobial Properties of Novel Silver/Polyrhodanine Nanofibers

Hyeyoung Kong and Jyongsik Jang
Web Release Date: Fri, 5 Sep 2008 00:00:00 EDT (Communication) DOI: 10.1021/bm800574x

Quelle: Biomacromolecules | 5 Sep 2008 | 6:00 am CEST

Polyhydroxyalkanoate Film Formation and Synthase Activity During In Vitro and In Situ Polymerization on Hydrophobic Surfaces

Shun Sato, Yusuke Ono, Yukiko Mochiyama, Easan Sivaniah, Yoshihiro Kikkawa, Kumar Sudesh, Tomohiro Hiraishi, Yoshiharu Doi, Hideki Abe, and Takeharu Tsuge
Web Release Date: Fri, 5 Sep 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800566s

Quelle: Biomacromolecules | 5 Sep 2008 | 6:00 am CEST

Novel Textile Chitosan Scaffolds Promote Spreading, Proliferation, and Differentiation of Osteoblasts

Christiane Heinemann, Sascha Heinemann, Anne Bernhardt, Hartmut Worch, and Thomas Hanke
Web Release Date: Fri, 5 Sep 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800693d

Quelle: Biomacromolecules | 5 Sep 2008 | 6:00 am CEST

Laccase-Induced Grafting on Plasma-Pretreated Polypropylene

M. Schroeder, E. Fatarella, J. Kovač, G. M. Guebitz, and V. Kokol
Web Release Date: Fri, 5 Sep 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800450b

Quelle: Biomacromolecules | 5 Sep 2008 | 6:00 am CEST

Synthesis and Evaluation of Globular Gd-DOTA-Monoamide Conjugates with Precisely Controlled Nanosizes for Magnetic Resonance Angiography

Todd Lyle Kaneshiro, Eun-Kee Jeong, Glen Morrell, Dennis L. Parker, and Zheng-Rong Lu
Web Release Date: Fri, 5 Sep 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800486c

Quelle: Biomacromolecules | 5 Sep 2008 | 6:00 am CEST

Cartilage Regeneration by Novel Polyethylene Oxide/Chitin/Chitosan Scaffolds

Yung-Chih Kuo and I-Nan Ku
Web Release Date: Fri, 5 Sep 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800651r

Quelle: Biomacromolecules | 5 Sep 2008 | 6:00 am CEST

Docking of molecules identified in bioactive medicinal plants extracts into the p50 NF-kappaB transcription factor: correlation with inhibition of NF-kappaB/DNA interactions and inhibitory effects on IL-8 gene expression

Background: The transcription factor NF-kappaB is a very interesting target molecule for the design on anti-tumor, anti-inflammatory and pro-apoptotic drugs. However, the application of the widely-used molecular docking computational method for the virtual screening of chemical libraries on NF-kappaB is not yet reported in literature. Docking studies on a dataset of 27 molecules from extracts of two different medicinal plants to NF-kappaB-p50 were performed with the purpose of developing a docking protocol fit for the target under study. Results: We enhanced the simple docking procedure by means of a sort of combined target- and ligand-based drug design approach. Advantages of this combination strategy, based on a similarity parameter for the identification of weak binding chemical entities, are illustrated in this work with the discovery of a new lead compound for NF-kappaB. Further biochemical analyses based on EMSA were performed and biological effects were tested on the compound exhibiting the best docking score. All experimental analysis were in fairly good agreement with molecular modeling findings. Conclusion: The results obtained sustain the concept that the docking performance is predictive of a biochemical activity. In this respect, this paper represents the first example of successfully individuation through molecular docking simulations of a promising lead compound for the inhibition of NF-kappaB-p50 biological activity and modulation of the expression of the NF-kB regulated IL8 gene.

Quelle: BMC Structural Biology - Latest articles | 3 Sep 2008 | 12:00 am CEST

Preparation of Poly(ethylene glycol) Protected Nanoparticles with Variable Bioconjugate Ligand Density

Marian E. Gindy, Shengxiang Ji, Thomas R. Hoye, Athanassios Z. Panagiotopoulos, and Robert K. Prud’homme
Web Release Date: Sat, 30 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8002013

Quelle: Biomacromolecules | 30 Aug 2008 | 6:00 am CEST

Synthesis of Hydroxypropylcellulose-poly(acrylic acid) Particles with Semi-Interpenetrating Polymer Network Structure

Ying Chen, Dan Ding, Zhiqing Mao, Yafeng He, Yong Hu, Wei Wu, and Xiqun Jiang
Web Release Date: Sat, 30 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800484e

Quelle: Biomacromolecules | 30 Aug 2008 | 6:00 am CEST

Poly(ethylene glycol)-Containing Hydrogel Surfaces for Antifouling Applications in Marine and Freshwater Environments

Tobias Ekblad, Gunnar Bergström, Thomas Ederth, Sheelagh L. Conlan, Robert Mutton, Anthony S. Clare, Su Wang, Yunli Liu, Qi Zhao, Fraddry D’Souza, Glen T. Donnelly, Peter R. Willemsen, Michala E. Pettitt, Maureen E. Callow, James A. Callow, and Bo Liedberg
Web Release Date: Sat, 30 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800547m

Quelle: Biomacromolecules | 30 Aug 2008 | 6:00 am CEST

Stimuli-Responsive Zwitterionic Block Copolypeptides: Poly( N-isopropylacrylamide)- block-poly(lysine- co-glutamic acid)

Jingguo Li, Tao Wang, Dalin Wu, Xiuqiang Zhang, Jiatao Yan, Song Du, Yifei Guo, Jintao Wang, and Afang Zhang
Web Release Date: Fri, 29 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800394p

Quelle: Biomacromolecules | 29 Aug 2008 | 6:00 am CEST

Secondary Structure Formation and LCST Behavior of Short Elastin-Like Peptides

Harald Nuhn and Harm-Anton Klok
Web Release Date: Fri, 29 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800784y

Quelle: Biomacromolecules | 29 Aug 2008 | 6:00 am CEST

BioPEGylation of Polyhydroxyalkanoates: Influence on Properties and Satellite-Stem Cell Cycle

Helder Marçal, Nico S. Wanandy, Vorapat Sanguanchaipaiwong, Catherine E. Woolnough, Antonio Lauto, Stephen M. Mahler, and L. John R. Foster
Web Release Date: Fri, 29 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800418e

Quelle: Biomacromolecules | 29 Aug 2008 | 6:00 am CEST

Biodegradable Interpolyelectrolyte Complexes Based on Methoxy Poly(ethylene glycol)-b-poly(α,L-glutamic acid) and Chitosan

Kun Luo, Jingbo Yin, Zhijiang Song, Lei Cui, Bin Cao, and Xuesi Chen
Web Release Date: Fri, 29 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800767f

Quelle: Biomacromolecules | 29 Aug 2008 | 6:00 am CEST

Substrata Mechanical Stiffness Can Regulate Adhesion of Viable Bacteria

Jenny A. Lichter, M. Todd Thompson, Maricela Delgadillo, Takehiro Nishikawa, Michael F. Rubner, and Krystyn J. Van Vliet
Web Release Date: Thu, 28 Aug 2008 00:00:00 EDT (Addition/Correction) DOI: 10.1021/bm8009335

Quelle: Biomacromolecules | 28 Aug 2008 | 6:00 am CEST

Electrodissolution of Inorganic Ions/DNA Multilayer Film for Tunable DNA Release

Fuan Wang, Dan Li, Gaiping Li, Xiaoqing Liu, and Shaojun Dong
Web Release Date: Thu, 28 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800766t

Quelle: Biomacromolecules | 28 Aug 2008 | 6:00 am CEST

DNA Interaction with Antitumor Polyamine Analogues: A Comparison with Biogenic Polyamines

C. N. N’soukpoé-Kossi, A. Ahmed Ouameur, T. Thomas, A. Shirahata, T. J. Thomas, and H. A. Tajmir-Riahi
Web Release Date: Tue, 26 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800412r

Quelle: Biomacromolecules | 26 Aug 2008 | 6:00 am CEST

Manipulating DNA Probe Presentation via Enzymatic Cleavage of Diluent Strands

Christopher K. Tison and Valeria T. Milam
Web Release Date: Thu, 21 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800497g

Quelle: Biomacromolecules | 21 Aug 2008 | 6:00 am CEST

Development of a Sialic Acid-Containing Hydrogel of Poly[N-(2-hydroxypropyl) methacrylamide]: Characterization and Implantation Study

Stéphane Woerly, Sébastien Fort, Isabelle Pignot-Paintrand, Cécile Cottet, Carole Carcenac, and Marc Savasta
Web Release Date: Thu, 21 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800234r

Quelle: Biomacromolecules | 21 Aug 2008 | 6:00 am CEST

Functionalization of Magnetic Nanowires by Charged Biopolymers

D. Magnin, V. Callegari, S. Mátéfi-Tempfli, M. Mátéfi-Tempfli, K. Glinel, A. M. Jonas, and S. Demoustier-Champagne
Web Release Date: Thu, 21 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8005402

Quelle: Biomacromolecules | 21 Aug 2008 | 6:00 am CEST

Formation of Brown Lines in Paper: Characterization of Cellulose Degradation at the Wet−Dry Interface

Zied Souguir, Anne-Laurence Dupont, and E. René de la Rie
Web Release Date: Thu, 21 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8006067

Quelle: Biomacromolecules | 21 Aug 2008 | 6:00 am CEST

Self-Assembling Peptide-Polymer Hydrogels Designed From the Coiled Coil Region of Fibrin

Peng Jing, Jai S. Rudra, Andrew B. Herr, and Joel H. Collier
Web Release Date: Wed, 20 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800459v

Quelle: Biomacromolecules | 20 Aug 2008 | 6:00 am CEST

Single-Walled Carbon Nanotube as a Unique Scaffold for the Multivalent Display of Sugars

Lingrong Gu, Pengju G. Luo, Haifang Wang, Mohammed J. Meziani, Yi Lin, L. Monica Veca, Li Cao, Fushen Lu, Xin Wang, Robert A. Quinn, Wei Wang, Puyu Zhang, Sebastian Lacher, and Ya-Ping Sun
Web Release Date: Wed, 20 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800395e

Quelle: Biomacromolecules | 20 Aug 2008 | 6:00 am CEST

Coniferyl Ferulate Incorporation into Lignin Enhances the Alkaline Delignification and Enzymatic Degradation of Cell Walls

John H. Grabber, Ronald D. Hatfield, Fachuang Lu, and John Ralph
Web Release Date: Wed, 20 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800528f

Quelle: Biomacromolecules | 20 Aug 2008 | 6:00 am CEST

Thiol/Acrylate-Modified PEO-PPO-PEO Triblocks Used as Reactive and Thermosensitive Copolymers

Guoguang Niu, Hongbin Zhang, Li Song, Xiaopeng Cui, Hui Cao, Yudong Zheng, Siquan Zhu, Zhou Yang, and Huai Yang
Web Release Date: Tue, 19 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800573e

Quelle: Biomacromolecules | 19 Aug 2008 | 6:00 am CEST

Conformational and Orientational Transformation of Silk Proteins in the Major Ampullate Gland of Nephila clavipes Spiders

Thierry Lefèvre, Simon Boudreault, Conrad Cloutier, and Michel Pézolet
Web Release Date: Fri, 15 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800390j

Quelle: Biomacromolecules | 15 Aug 2008 | 6:00 am CEST

Mechanical Properties of C-5 Epimerized Alginates

Ý. A. Mørch, S. Holtan, I. Donati, B. L. Strand, and G. Skjåk-Bræk
Web Release Date: Fri, 15 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8003572

Quelle: Biomacromolecules | 15 Aug 2008 | 6:00 am CEST

Fabrication and Characterization of Electrospun Chitosan Nanofibers Formed via Templating with Polyethylene Oxide

Satyajeet S. Ojha, Derrick R. Stevens, Torissa J. Hoffman, Kelly Stano, Rebecca Klossner, Mary C. Scott, Wendy Krause, Laura I. Clarke, and Russell E. Gorga
Web Release Date: Fri, 15 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800551q

Quelle: Biomacromolecules | 15 Aug 2008 | 6:00 am CEST

Solid-Phase Chemical Amination of a Lipase from Bacillus thermocatenulatus To Improve Its Stabilization via Covalent Immobilization on Highly Activated Glyoxyl-Agarose

Gloria Fernandez-Lorente, Cesar A. Godoy, Adriano A. Mendes, Fernando Lopez-Gallego, Valeria Grazu, Blanca de las Rivas, Jose M. Palomo, Juan Hermoso, Roberto Fernandez-Lafuente, and Jose M. Guisan
Web Release Date: Fri, 15 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800609g

Quelle: Biomacromolecules | 15 Aug 2008 | 6:00 am CEST

Intrinsically Antibacterial Materials Based on Polymeric Derivatives of Eugenol for Biomedical Applications

Luis Rojo, Jose. M. Barcenilla, Blanca Vázquez, Ramón González, and Julio San Román
Web Release Date: Fri, 15 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800570u

Quelle: Biomacromolecules | 15 Aug 2008 | 6:00 am CEST

Morphological Control of Poly(ethylene glycol)-block-poly(ε-caprolactone) Copolymer Aggregates in Aqueous Solution

Nichole Fairley, Bryan Hoang, and Christine Allen
Web Release Date: Fri, 15 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800572p

Quelle: Biomacromolecules | 15 Aug 2008 | 6:00 am CEST

J- and H-Aggregates of 5,10,15,20-Tetrakis-(4-sulfonatophenyl)-porphyrin and Interconversion in PEG-b-P4VP Micelles

Lizhi Zhao, Rujiang Ma, Junbo Li, Yan Li, Yingli An, and Linqi Shi
Web Release Date: Thu, 14 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8004808

Quelle: Biomacromolecules | 14 Aug 2008 | 6:00 am CEST

Microrheology of Hyaluronan Solutions: Implications for the Endothelial Glycocalyx

Nadja Nijenhuis, Daisuke Mizuno, Christoph F. Schmidt, Hans Vink, and Jos A. E. Spaan
Web Release Date: Thu, 14 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800381z

Quelle: Biomacromolecules | 14 Aug 2008 | 6:00 am CEST

Advances on Selective C-6 Oxidation of Chitosan by TEMPO

Nicolas Bordenave, Stéphane Grelier, and Véronique Coma
Web Release Date: Thu, 14 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800375v

Quelle: Biomacromolecules | 14 Aug 2008 | 6:00 am CEST

Suppression of Insulin Aggregation by Heparin

Katie Giger, Ram P. Vanam, Emek Seyrek, and Paul L. Dubin
Web Release Date: Wed, 13 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8002557

Quelle: Biomacromolecules | 13 Aug 2008 | 6:00 am CEST

Low Molecular Weight Polyethylenimine Grafted N-Maleated Chitosan for Gene Delivery: Properties and In Vitro Transfection Studies

Bo Lu, Xiao-Ding Xu, Xian-Zheng Zhang, Si-Xue Cheng, and Ren-Xi Zhuo
Web Release Date: Wed, 13 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8004676

Quelle: Biomacromolecules | 13 Aug 2008 | 6:00 am CEST

Electroactive Aniline Pentamer Cross-Linking Chitosan for Stimulation Growth of Electrically Sensitive Cells

Jun Hu, Lihong Huang, Xiuli Zhuang, Peibiao Zhang, Le Lang, Xuesi Chen, Yen Wei, and Xiabin Jing
Web Release Date: Wed, 13 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800705t

Quelle: Biomacromolecules | 13 Aug 2008 | 6:00 am CEST

Amphiphilic Core−Shell Nanocarriers Based On Hyperbranched Poly(ester amide)-star-PCL: Synthesis, Characterization, and Potential as Efficient Phase Transfer Agent

Ying Lin, Xiaohui Liu, Zhongmin Dong, Baixiang Li, Xuesi Chen, and Yue-Sheng Li
Web Release Date: Wed, 13 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800607a

Quelle: Biomacromolecules | 13 Aug 2008 | 6:00 am CEST

Biodegradable Thermoplastic Polyurethanes Incorporating Polyhedral Oligosilsesquioxane

Pamela T. Knight, Kyung Min Lee, Haihu Qin, and Patrick T. Mather
Web Release Date: Wed, 13 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8004935

Quelle: Biomacromolecules | 13 Aug 2008 | 6:00 am CEST

Biomimetic Mineralization Induced by Fibrils of Polymers Derived from a Bile Acid

Xu Zhang, Zhanyong Li, and X. X. Zhu
Web Release Date: Wed, 13 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800204t

Quelle: Biomacromolecules | 13 Aug 2008 | 6:00 am CEST

Structure of Heat-Induced β-Lactoglobulin Aggregates and their Complexes with Sodium-Dodecyl Sulfate

Jin-Mi Jung, Gabriela Savin, Matthieu Pouzot, Christophe Schmitt, and Raffaele Mezzenga
Web Release Date: Wed, 13 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800502j

Quelle: Biomacromolecules | 13 Aug 2008 | 6:00 am CEST

Plasmid DNA Binds to the Core Oligosaccharide Domain of LPS Molecules of E. coli Cell Surface in the CaCl2-Mediated Transformation Process

Subrata Panja, Pulakesh Aich, Bimal Jana, and Tarakdas Basu
Web Release Date: Wed, 13 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8005215

Quelle: Biomacromolecules | 13 Aug 2008 | 6:00 am CEST

Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces

Background: Many studies have examined rules governing two aspects of protein structures: short segments and proteins' structural domains. Nevertheless, the organization and nature of the conformational space of segments with intermediate length between short segments and domains remain unclear. Conformational spaces of intermediate length segments probably differ from those of short segments. We investigated the identification and characterization of the boundary(s) between peptide-like (short segment) and protein-like (long segment) distributions. We generated ensembles embedded in globular proteins comprising segments 10–50 residues long. We explored the relationships between the conformational distribution of segments and their lengths, and also protein structural classes using principal component analysis based on the intra-segment Cα-Cα atomic distances. Results: Our statistical analyses of segment conformations and length revealed critical dual transitions in their conformational distribution with segments derived from all four structural classes. Dual transitions were identified with the intermediate phase between the short segments and domains. Consequently, protein segment universes were categorized. i) Short segments (10–22 residues) showed a distribution with a high frequency of secondary structure clusters. ii) Medium segments (23–26 residues) showed a distribution corresponding to an intermediate state of transitions. iii) Long segments (27–50 residues) showed a distribution converging on one huge cluster containing compact conformations with a smaller radius of gyration. This distribution reflects the protein structures' organization and protein domains' origin. Three major conformational components (radius of gyration, structural symmetry with respect to the N-terminal and C-terminal halves, and single-turn/two-turn structure) well define most of the segment universes. Furthermore, we identified several conformational components that were unique to each structural class. Those characteristics suggest that protein segment conformation is described by compositions of the three common structural variables with large contributions and specific structural variables with small contributions. Conclusion: The present results of the analyses of four protein structural classes show the universal role of three major components as segment conformational descriptors. The obtained perspectives of distribution changes related to the segment lengths using the three key components suggest both the adequacy and the possibility of further progress on the prediction strategies used in the recent de novo structure-prediction methods.

Quelle: BMC Structural Biology - Latest articles | 13 Aug 2008 | 12:00 am CEST

Biomacromolecules

Biomacromolecules, Volume 9 Issue 8 (August 2008) is now available

Quelle: Biomacromolecules | 11 Aug 2008 | 6:00 am CEST

Contact prediction in protein modeling: Scoring, folding and refinement of coarse-grained models

Background: Several different methods for contact prediction succeeded within the Sixth Critical Assessment of Techniques for Protein Structure Prediction (CASP6). The most relevant were non-local contact predictions for targets from the most difficult categories: fold recognition-analogy and new fold. Such contacts could provide valuable structural information in case a template structure cannot be found in the PDB. Results: We described comprehensive tests of the effectiveness of contact data in various aspects of de novo modeling with CABS, an algorithm which was used successfully in CASP6 by the Kolinski-Bujnicki group. We used the predicted contacts in a simple scoring function for the post-simulation ranking of protein models and as a soft bias in the folding simulations and in the fold-refinement procedure. The latter approach turned out to be the most successful. The CABS force field used in the Replica Exchange Monte Carlo simulations cooperated with the true contacts and discriminated the false ones, which resulted in an improvement of the majority of Kolinski-Bujnicki's protein models. In the modeling we tested different sets of predicted contact data submitted to the CASP6 server. According to our results, the best performing were the contacts with the accuracy balanced with the coverage, obtained either from the best two predictors only or by a consensus from as many predictors as possible. Conclusion: Our tests have shown that theoretically predicted contacts can be very beneficial for protein structure prediction. Depending on the protein modeling method, a contact data set applied should be prepared with differently balanced coverage and accuracy of predicted contacts. Namely, high coverage of contact data is important for the model ranking and high accuracy for the folding simulations.

Quelle: BMC Structural Biology - Latest articles | 11 Aug 2008 | 12:00 am CEST

Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans

Background: There are considerable differences between bacterial and mammalian glycans. In contrast to most eukaryotic carbohydrates, bacterial glycans are often composed of repeating units with diverse functions ranging from structural reinforcement to adhesion, colonization and camouflage. Since bacterial glycans are typically displayed at the cell surface, they can interact with the environment and, therefore, have significant biomedical importance. Results: The sequence characteristics of glycans (monosaccharide composition, modifications, and linkage patterns) for the higher bacterial taxonomic classes have been examined and compared with the data for mammals, with both similarities and unique features becoming evident. Compared to mammalian glycans, the bacterial glycans deposited in the current databases have a more than ten-fold greater diversity at the monosaccharide level, and the disaccharide pattern space is approximately nine times larger. Specific bacterial subclasses exhibit characteristic glycans which can be distinguished on the basis of distinctive structural features or sequence properties. Conclusions: For the first time a systematic database analysis of the bacterial glycome has been performed. This study summarizes the current knowledge of bacterial glycan architecture and diversity and reveals putative targets for the rational design and development of therapeutic intervention strategies by comparing bacterial and mammalian glycans.

Quelle: BMC Structural Biology - Latest articles | 11 Aug 2008 | 12:00 am CEST

Synthesis and Biological Evaluation of a Polysialic Acid-Based Hydrogel as Enzymatically Degradable Scaffold Material for Tissue Engineering

Silke Berski, Jeroen van Bergeijk, David Schwarzer, Yvonne Stark, Cornelia Kasper, Thomas Scheper, Claudia Grothe, Rita Gerardy-Schahn, Andreas Kirschning, and Gerald Dräger
Web Release Date: Sat, 9 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800327s

Quelle: Biomacromolecules | 9 Aug 2008 | 6:00 am CEST

Biomimetic Carbohydrate Substrates of Tunable Properties Using Immobilized Dextran Hydrogels

Mark H. Lee, David Boettiger, and Russell J. Composto
Web Release Date: Fri, 8 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8002094

Quelle: Biomacromolecules | 8 Aug 2008 | 6:00 am CEST

Differentiation of Osteoblasts on Pectin-Coated Titanium

H. Kokkonen, C. Cassinelli, R. Verhoef, M. Morra, H. A. Schols, and J. Tuukkanen
Web Release Date: Tue, 5 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800356b

Quelle: Biomacromolecules | 5 Aug 2008 | 6:00 am CEST

Spin-On End-Functional Diblock Copolymers for Quantitative DNA Immobilization

Lu Chen, Hernán R. Rengifo, Cristian Grigoras, Xiaoxu Li, Zengmin Li, Jingyue Ju, and Jeffrey T. Koberstein
Web Release Date: Tue, 5 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800258g

Quelle: Biomacromolecules | 5 Aug 2008 | 6:00 am CEST

Colorimetric Enzymatic Activity Assay Based on Noncrosslinking Aggregation of Gold Nanoparticles Induced by Adsorption of Substrate Peptides

Jun Oishi, Yoji Asami, Takeshi Mori, Jeong-Hun Kang, Takuro Niidome, and Yoshiki Katayama
Web Release Date: Tue, 5 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800192d

Quelle: Biomacromolecules | 5 Aug 2008 | 6:00 am CEST

Design of a Synthetic Collagen-Binding Peptidoglycan that Modulates Collagen Fibrillogenesis

John E. Paderi and Alyssa Panitch
Web Release Date: Tue, 5 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm8006852

Quelle: Biomacromolecules | 5 Aug 2008 | 6:00 am CEST

Synthesis and Rheological Properties of Responsive Thickeners Based on Polysaccharide Architectures

C. Karakasyan, S. Lack, F. Brunel, P. Maingault, and D. Hourdet
Web Release Date: Sat, 2 Aug 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800393s

Quelle: Biomacromolecules | 2 Aug 2008 | 6:00 am CEST

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

Background: Automatic protein modelling pipelines are becoming ever more accurate; this has come hand in hand with an increasingly complicated interplay between all components involved. Nevertheless, there are still potential improvements to be made in template selection, refinement and protein model selection. Results: In the context of an automatic modelling pipeline, we analysed each step separately, revealing several non-intuitive trends and explored a new strategy for protein conformation sampling using Genetic Algorithms (GA). We apply the concept of alternating evolutionary pressure (AEP), i.e. intermediate rounds within the GA runs where unrestrained, linear growth of the model populations is allowed. Conclusion: This approach improves the overall performance of the GA by allowing models to overcome local energy barriers. AEP enabled the selection of the best models in 40% of all targets; compared to 25% for a normal GA.

Quelle: BMC Structural Biology - Latest articles | 1 Aug 2008 | 12:00 am CEST

Synthesis and Optimization of Gelatin Nanoparticles Using the Miniemulsion Process

Anitha Ethirajan, Katrin Schoeller, Anna Musyanovych, Ulrich Ziener, and Katharina Landfester
Web Release Date: Thu, 31 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800377w

Quelle: Biomacromolecules | 31 Jul 2008 | 6:00 am CEST

Water-Induced Hydrophobicity of Soy Protein Materials Containing 2,2-Diphenyl-2-hydroxyethanoic Acid

Rakesh Kumar and Lina Zhang
Web Release Date: Thu, 31 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800396x

Quelle: Biomacromolecules | 31 Jul 2008 | 6:00 am CEST

Kinetic Controlled Synthesis of pH-Responsive Network Alginate

Ariel W. Chan, Ralph A. Whitney, and Ronald J. Neufeld
Web Release Date: Thu, 31 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800594f

Quelle: Biomacromolecules | 31 Jul 2008 | 6:00 am CEST

Biopolymer and Water Dynamics in Microbial Biofilm Extracellular Polymeric Substance

Jennifer A. Hornemann, Anna A. Lysova, Sarah L. Codd, Joseph D. Seymour, Scott C. Busse, Philip S. Stewart, and Jennifer R. Brown
Web Release Date: Wed, 30 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800269h

Quelle: Biomacromolecules | 30 Jul 2008 | 6:00 am CEST

Functionalized Amphiphilic Hyperbranched Polymers for Targeted Drug Delivery

Si Chen, Xian-Zheng Zhang, Si-Xue Cheng, Ren-Xi Zhuo, and Zhong-Wei Gu
Web Release Date: Wed, 30 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800371n

Quelle: Biomacromolecules | 30 Jul 2008 | 6:00 am CEST

Self-Cross-Linking Polyelectrolyte Complexes for Therapeutic Cell Encapsulation

M. A. Jafar Mazumder, Feng Shen, Nicholas A. D. Burke, Murray A. Potter, and Harald D. H. Stöver
Web Release Date: Wed, 30 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800580c

Quelle: Biomacromolecules | 30 Jul 2008 | 6:00 am CEST

Pentalysine-Grafted ROMP Polymers for DNA Complexation and Delivery

Rebecca B. Breitenkamp and Todd Emrick
Web Release Date: Wed, 30 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800511p

Quelle: Biomacromolecules | 30 Jul 2008 | 6:00 am CEST

Ring-Shaped Assembly of Microtubules Shows Preferential Counterclockwise Motion

Ryuzo Kawamura, Akira Kakugo, Kazuhiro Shikinaka, Yoshihito Osada, and Jian Ping Gong
Web Release Date: Tue, 29 Jul 2008 00:00:00 EDT (Communication) DOI: 10.1021/bm800639w

Quelle: Biomacromolecules | 29 Jul 2008 | 6:00 am CEST

Biodegradable Amphiphilic Copolymers Based on Poly(ϵ-caprolactone)-Graft Chondroitin Sulfate as Drug Carriers

Ai-Ling Chen, Hsiao-Chen Ni, Li-Fang Wang, and Jenn-Shing Chen
Web Release Date: Tue, 29 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800485x

Quelle: Biomacromolecules | 29 Jul 2008 | 6:00 am CEST

Synthesis of Bioinorganic Antimicrobial Peptide Nanoparticles with Potential Therapeutic Properties

D. Matthew Eby, Karen E. Farrington, and Glenn R. Johnson
Web Release Date: Tue, 29 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800512e

Quelle: Biomacromolecules | 29 Jul 2008 | 6:00 am CEST

Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase

Background: In search of new antifungal targets of potential interest for pharmaceutical companies, we initiated a comparative genomics study to identify the most promising protein-coding genes in fungal genomes. One criterion was the protein sequence conservation between reference pathogenic genomes. A second criterion was that the corresponding gene in Saccharomyces cerevisiae should be essential. Since thiamine pyrophosphate is an essential product involved in a variety of metabolic pathways, proteins responsible for its production satisfied these two criteria. Results: We report the enzymatic characterization and the crystallographic structure of the Candida albicans Thiamine pyrophosphokinase. The protein was co-crystallized with thiamine or thiamine-PNP. Conclusion: The presence of an inorganic phosphate in the crystallographic structure opposite the known AMP binding site relative to the thiamine moiety suggests that a second AMP molecule could be accommodated in the C. albicans structure. Together with the crystallographic structures of the enzyme/substrate complexes this suggests the existence of a secondary, less specific, nucleotide binding site in the Candida albicans thiamine pyrophosphokinase which could transiently serve during the release or the binding of ATP. The structures also highlight a conserved Glutamine residue (Q138) which could interact with the ATP α-phosphate and act as gatekeeper. Finally, the TPK/Thiamine-PNP complex is consistent with a one step mechanism of pyrophosphorylation.

Quelle: BMC Structural Biology - Latest articles | 24 Jul 2008 | 12:00 am CEST

Technique of Surface Modification of a Cell-Adhesion-Resistant Hydrogel by a Cell-Adhesion-Available Inorganic Microarray

Jianguo Sun, Stefan V. Graeter, Lin Yu, Shifeng Duan, Joachim P. Spatz, and Jiandong Ding
Web Release Date: Wed, 23 Jul 2008 00:00:00 EDT (Communication) DOI: 10.1021/bm800477s

Quelle: Biomacromolecules | 23 Jul 2008 | 6:00 am CEST

Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: Mechanistic implications

Background: Urate oxidase (EC 1.7.3.3 or UOX) catalyzes the conversion of uric acid and gaseous molecular oxygen to 5-hydroxyisourate and hydrogen peroxide, in the absence of cofactor or particular metal cation. The functional enzyme is a homo-tetramer with four active sites located at dimeric interfaces. Results: The catalytic mechanism was investigated through a ternary complex formed between the enzyme, uric acid, and cyanide that stabilizes an intermediate state of the reaction. When uric acid is replaced by a competitive inhibitor, no complex with cyanide is formed. Conclusion: The X-ray structure of this compulsory ternary complex led to a number of mechanistic evidences that support a sequential mechanism in which the two reagents, dioxygen and a water molecule, process through a common site located 3.3 Ã… above the mean plane of the ligand. This site is built by the side chains of Asn 254, and Thr 57, two conserved residues belonging to two different subunits of the homo-tetramer. The absence of a ternary complex between the enzyme, a competitive inhibitor, and cyanide suggests that cyanide inhibits the hydroxylation step of the reaction, after the initial formation of a hydroperoxyde type intermediate.

Quelle: BMC Structural Biology - Latest articles | 20 Jul 2008 | 12:00 am CEST

Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure

Background: Although multiple templates are frequently used in comparative modeling, the effect of inclusion of additional template(s) on model accuracy (when compared to that of corresponding single-template based models) is not clear. To address this, we systematically analyze two-template models, the simplest case of multiple-template modeling. For an existing target-template pair (single-template modeling), a two-template based model of the target sequence is constructed by including an additional template without changing the original alignment to measure the effect of the second template on model accuracy. Results: Even though in a large number of cases a two-template model showed higher accuracy than the corresponding one-template model, over the entire dataset only a marginal improvement was observed on average, as there were many cases where no change or the reverse change was observed. The increase in accuracy due to the structural complementarity of the templates increases at higher alignment accuracies. The combination of templates showing the highest potential for improvement is that where both templates share similar and low (less than 30%) sequence identity with the target, as well as low sequence identity with each other. The structural similarity between the templates also helps in identifying template combinations having a higher chance of resulting in an improved model. Conclusion: Inclusion of additional template(s) does not necessarily improve model quality, but there are distinct combinations of the two templates, which can be selected a priori, that tend to show improvement in model quality over the single template model. The benefit derived from the structural complementarity is dependent on the accuracy of the modeling alignment. The study helps to explain the observation that a careful selection of templates together with an accurate target:template alignment are necessary to the benefit from using multiple templates in comparative modeling and provides guidelines to maximize the benefit from using multiple templates. This enables formulation of simple template selection rules to rank targets of a protein family in the context of structural genomics.

Quelle: BMC Structural Biology - Latest articles | 16 Jul 2008 | 12:00 am CEST

Facile Preparation of Well-Defined AB2 Y-Shaped Miktoarm Star Polypeptide Copolymer via the Combination of Ring-Opening Polymerization and Click Chemistry

Jingyi Rao, Yanfeng Zhang, Jingyan Zhang, and Shiyong Liu
Web Release Date: Wed, 9 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/bm800462q

Quelle: Biomacromolecules | 9 Jul 2008 | 6:00 am CEST

Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

Background: The Ambiguous Restraints for Iterative Assignment (ARIA) approach is widely used for NMR structure determination. It is based on simultaneously calculating structures and assigning NOE through an iterative protocol. The final solution consists of a set of conformers and a list of most probable assignments for the input NOE peak list. Results: ARIA was extended with a series of graphical tools to facilitate a detailed analysis of the intermediate and final results of the ARIA protocol. These additional features provide (i) an interactive contact map, serving as a tool for the analysis of assignments, and (ii) graphical representations of structure quality scores and restraint statistics. The interactive contact map between residues can be clicked to obtain information about the restraints and their contributions. Profiles of quality scores are plotted along the protein sequence, and contact maps provide information of the agreement with the data on a residue pair level. Conclusion: The graphical tools and outputs described here significantly extend the validation and analysis possibilities of NOE assignments given by ARIA as well as the analysis of the quality of the final structure ensemble. These tools are included in the latest version of ARIA, which is available at http://aria.pasteur.fr. The Web site also contains an installation guide, a user manual and example calculations.

Quelle: BMC Structural Biology - Latest articles | 5 Jun 2008 | 12:00 am CEST

Protecting role of cosolvents in protein denaturation by SDS: a structural study

Background: Recently, we reported a unique approach to preserve the activity of some proteins in the presence of the denaturing agent, Sodium Dodecyl Sulfate (SDS). This was made possible by addition of the amphipathic solvent 2,4-Methyl-2-PentaneDiol (MPD), used as protecting but also as refolding agent for these proteins. Although the persistence of the protein activity in the SDS/MPD mixture was clearly established, preservation of their structure was only speculative until now. Results: In this paper, a detailed X-ray study addresses the pending question. Crystals of hen egg-white lysozyme were grown for the first time in the presence of MPD and denaturing concentrations of SDS. Depending on crystallization conditions, tetragonal crystals in complex with either SDS or MPD were collected. The conformation of both structures was very similar to the native lysozyme and the obtained complexes of SDS-lysozyme and MPD-lysozyme give some insights in the interplay of protein-SDS and protein-MPD interactions. Conclusion: This study clearly established the preservation of the enzyme structure in a SDS/MPD mixture. It is hypothesized that high concentrations of MPD would change the properties of SDS and lower or avoid interactions between the denaturant and the protein. These structural data therefore support the hypothesis that MPD avoids disruption of the enzyme structure by SDS and can protect proteins from SDS denaturation.

Quelle: BMC Structural Biology - Latest articles | 3 Jun 2008 | 12:00 am CEST