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journal of biological chemistry

Song-Ho Chong, Prathit Chatterjee, Sihyun Ham
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields...
February 6, 2017: Annual Review of Physical Chemistry
Christopher T Walsh
After an undergraduate degree in biology at Harvard, I started graduate school at The Rockefeller Institute for Medical Research in New York City in July 1965. I was attracted to the chemical side of biochemistry and joined Fritz Lipmann's large, hierarchical laboratory to study enzyme mechanisms. That work led to postdoctoral research with Robert Abeles at Brandeis, then a center of what, 30 years later, would be called chemical biology. I spent 15 years on the Massachusetts Institute of Technology faculty, in both the Chemistry and Biology Departments, and then 26 years on the Harvard Medical School Faculty...
January 11, 2017: Annual Review of Biochemistry
Timothy L Fletcher, Paul L A Popelier
Continuing the development of the FFLUX, a multipolar polarizable force field driven by machine learning, we present a modern approach to atom-typing and building transferable models for predicting atomic properties in proteins. Amino acid atomic charges in a peptide chain respond to the substitution of a neighboring residue and this response can be categorized in a manner similar to atom-typing. Using a machine learning method called kriging, we are able to build predictive models for an atom that is defined, not only by its local environment, but also by its neighboring residues, for a minimal additional computational cost...
March 5, 2017: Journal of Computational Chemistry
Fouad S Husseini, David Robinson, Neil T Hunt, Anthony W Parker, Jonathan D Hirst
The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well-characterized proteins, representing a range of structural types...
November 21, 2016: Journal of Computational Chemistry
James C Campbell, Alexander Tischer, Venkata Machha, Laurie Moon-Tasson, Banumathi Sankaran, Choel Kim, Matthew Auton
von Willebrand factor׳s (VWF) primary hemostatic responsibility is to deposit platelets at sites of vascular injury to prevent bleeding. This function is mediated by the interaction between the VWF A1 domain and the constitutively active platelet receptor, GPIbα. The crystal structure of the A1 domain harboring the von Willebrand disease (vWD) type 2M mutation p.Gly1324Ser has been recently published in the Journal of Biological Chemistry describing its effect on the function and structural stability of the A1 domain of VWF, "Mutational constraints on local unfolding inhibit the rheological adaptation of von Willebrand factor" [1]...
June 2016: Data in Brief
Jon W Wong, Jian Wang, Julie Kowalski
No abstract text is available yet for this article.
August 10, 2016: Journal of Agricultural and Food Chemistry
Isidro Cortes-Ciriano
Compound physicochemical properties favoring in vitro potency are not always correlated to desirable pharmacokinetic profiles. Therefore, using potency (i.e., IC50) as the main criterion to prioritize candidate drugs at early stage drug discovery campaigns has been questioned. Yet, the vast majority of the virtual screening models reported in the medicinal chemistry literature predict the biological activity of compounds by regressing in vitro potency on topological or physicochemical descriptors. Two studies published in this journal showed that higher predictive power on external molecules can be achieved by using ligand efficiency indices as the dependent variable instead of a metric of potency (IC50) or binding affinity (Ki)...
August 22, 2016: Journal of Chemical Information and Modeling
Lila M Gierasch
No abstract text is available yet for this article.
July 1, 2016: Journal of Biological Chemistry
Zsolt Szűcs, Magdolna Csávás, Erzsébet Rőth, Anikó Borbás, Gyula Batta, Florent Perret, Eszter Ostorházi, Réka Szatmári, Evelien Vanderlinden, Lieve Naesens, Pál Herczegh
A series of lipophilic teicoplanin pseudoaglycon derivatives, including alkyl-, aryl-, calixarene- and protected sugar-containing conjugates, were prepared using azide-alkyne click chemistry. Out of the conditions applied, the CuSO4-ascorbate reagent system proved to be more efficient than the Cu(I)I-Et3N-mediated reaction. Some of the new compounds have high in vitro activity against glycopeptide-resistant Gram-positive bacteria, including vanA-positive Enterococcus faecalis. A few of them also display promising in vitro anti-influenza activity...
February 2017: Journal of Antibiotics
Hiroyuki Osada
The research on antibiotics requires the integration of broad areas, such as microbiology, organic chemistry, biochemistry and pharmacology. It is similar to the field of chemical biology that is recently popular as an approach for drug discovery. When we isolate a new compound from a microorganism, we can pursue the interesting research on chemistry and biology. In this review, I would like to introduce our achievements in relation to reveromycin A.The Journal of Antibiotics advance online publication, 8 June 2016; doi:10...
June 8, 2016: Journal of Antibiotics
International Journal Of Molecular Sciences Editorial Office
TheEditorsoftheInternationalJournalofMolecularScienceshaveestablishedtheBestPaperAward to recognize the most outstanding articles published in the areas of molecular biology, molecular physics and chemistry that have been published in the International Journal of Molecular Sciences.[...].
May 20, 2016: International Journal of Molecular Sciences
Yunlin Zhang, Xiaolong Yao, Boqiang Qin
Lake Taihu, as the important drinking water source of the Yangtze River Delta urban agglomeration and the third largest freshwater lake in China, has experienced serious lake eutrophication and water quality deterioration in the past three decades. Growing scientific, political, and public attention has been given to the water quality of Lake Taihu. This study aimed to conduct a comparative quantitative and qualitative analysis of the development, current hotspots, and future directions of Lake Taihu research using a bibliometric analysis of eight well-studied lakes (Lake Taihu, Lake Baikal, Lake Biwa, Lake Erie, Lake Michigan, Lake Ontario, Lake Superior and Lake Victoria) around the world based on the Science Citation Index (SCI) database...
July 2016: Environmental Science and Pollution Research International
Norma M Allewell
The biofilms that many bacteria and fungi produce enable them to form communities, adhere tightly to surfaces, evade host immunity, and resist antibiotics. Pathogenic microorganisms that form biofilms are very difficult to eradicate and thus are a frequent source of life-threatening, hospital-acquired infections. This series of five minireviews from the Journal of Biological Chemistry provides a broad overview of our current understanding of biofilms and the challenges that remain. The structure, biosynthesis, and biological function of the biofilms produced by pathogenic fungi are the subject of the first article, by Sheppard and Howell...
June 10, 2016: Journal of Biological Chemistry
Travis A Pemberton, David W Christianson
Terpenoid cyclases catalyze the most complex reactions in biology, in that more than half of the substrate carbon atoms often undergo changes in bonding during the course of a multistep cyclization cascade that proceeds through multiple carbocation intermediates. Many cyclization mechanisms require stereospecific deprotonation and reprotonation steps, and most cyclization cascades are terminated by deprotonation to yield an olefin product. The first bacterial terpenoid cyclase to yield a crystal structure was pentalenene synthase from Streptomyces exfoliatus UC5319...
July 2016: Journal of Antibiotics
Gregg E A Solomon, Stephen Carley, Alan L Porter
Interest in cross-disciplinary research knowledge interchange runs high. Review processes at funding agencies, such as the U.S. National Science Foundation, consider plans to disseminate research across disciplinary bounds. Publication in the leading multidisciplinary journals, Nature and Science, may signify the epitome of successful interdisciplinary integration of research knowledge and cross-disciplinary dissemination of findings. But how interdisciplinary are they? The journals are multidisciplinary, but do the individual articles themselves draw upon multiple fields of knowledge and does their influence span disciplines? This research compares articles in three fields (Cell Biology, Physical Chemistry, and Cognitive Science) published in a leading disciplinary journal in each field to those published in Nature and Science...
2016: PloS One
Joong-Youn Shim, Leepakshi Khurana, Debra A Kendall
Despite the important role of the carboxyl-terminus (Ct) of the activated brain cannabinoid receptor one (CB1) in the regulation of G protein signaling, a structural understanding of interactions with G proteins is lacking. This is largely due to the highly flexible nature of the CB1 Ct that dynamically adapts its conformation to the presence of G proteins. In the present study, we explored how the CB1 Ct can interact with the G protein by building on our prior modeling of the CB1-Gi complex (Shim, Ahn, and Kendall, The Journal of Biological Chemistry 2013;288:32449-32465) to incorporate a complete CB1 Ct (Glu416(Ct)-Leu472(Ct))...
April 2016: Proteins
Fidele Ntie-Kang, Leonel E Njume, Yvette I Malange, Stefan Günther, Wolfgang Sippl, Joseph N Yong
Traditional medicinal practices have a profound influence on the daily lives of people living in developing countries, particularly in Africa, since the populations cannot generally afford the cost of Western medicines. We have undertaken to investigate the correlation between the uses of plants in Traditional African medicine and the biological activities of the derived natural products, with the aim to validate the use of traditional medicine in Northern African communities. The literature is covered for the period 1959-2015 and part III of this review series focuses on plant families with names beginning with letters T to Z...
April 2016: Natural Products and Bioprospecting
Sanchita Hati, Sudeep Bhattacharyya
A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions...
March 2016: Biochemistry and Molecular Biology Education
Ryan P Womack
This study takes a stratified random sample of articles published in 2014 from the top 10 journals in the disciplines of biology, chemistry, mathematics, and physics, as ranked by impact factor. Sampled articles were examined for their reporting of original data or reuse of prior data, and were coded for whether the data was publicly shared or otherwise made available to readers. Other characteristics such as the sharing of software code used for analysis and use of data citation and DOIs for data were examined...
2015: PloS One
Emmanuel Drouin, Marie Drouin-Masson
A very large number of articles about vitalism have been published since 1894 in the journal Science. Vitalism is a theory according to which living organisms appear to possess something more than inanimate objects. The "vital principle" is minted in 1778 by Barthez in "Les nouveaux éléments de la science de l'homme", (Stahl talks of phlogiston for chemistry). In their view, the life of the whole is not the simple sum of the life of the components. Such a view was hatched in response to the Cartesian mechanist interpretation of living matter as proposed by Galileo and Descartes...
June 2015: Vesalius: Acta Internationales Historiae Medicinae
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