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https://www.readbyqxmd.com/read/27914049/modeling-binding-affinity-of-pathological-mutations-for-computational-protein-design
#1
Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
An important aspect of protein functionality is the formation of specific complexes with other proteins, which are involved in the majority of biological processes. The functional characterization of such interactions at molecular level is necessary, not only to understand biological and pathological phenomena but also to design improved, or even new interfaces, or to develop new therapeutic approaches. X-ray crystallography and NMR spectroscopy have increased the number of 3D protein complex structures deposited in the Protein Data Bank (PDB)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913358/conformational-sampling-of-a-biomolecular-rugged-energy-landscape
#2
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/27912054/inner-secrets-of-the-respirasome
#3
Andrew Melber, Dennis R Winge
Structure determination by cryo-electron microscopy has approached atomic resolution and helped solve structures of large membrane-protein complexes that resisted crystallography. The 4.0 Å cryo-EM structure of one of the most intricate enzyme systems, the respirasome, in the mitochondrial inner membrane is reported in this issue of Cell.
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27911811/the-structure-of-the-catechin-binding-site-of-human-sulfotransferase-1a1
#4
Ian Cook, Ting Wang, Mark Girvin, Thomas S Leyh
We are just beginning to understand the allosteric regulation of the human cytosolic sulfotransferase (SULTs) family-13 disease-relevant enzymes that regulate the activities of hundreds, if not thousands, of signaling small molecules. SULT1A1, the predominant isoform in adult liver, harbors two noninteracting allosteric sites, each of which binds a different molecular family: the catechins (naturally occurring flavonols) and nonsteroidal antiinflammatory drugs (NSAIDs). Here, we present the structure of an SULT allosteric binding site-the catechin-binding site of SULT1A1 bound to epigallocatechin gallate (EGCG)...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911011/fragment-based-design-synthesis-and-biological-evaluation-of-1-substituted-indole-2-carboxylic-acids-as-selective-mcl-1-inhibitors
#5
Ziqian Wang, Wenjie Xu, Ting Song, Zongwei Guo, Lu Liu, Yudan Fan, Anhui Wang, Zhichao Zhang
Based on a known selective Mcl-1 inhibitor, 6-chloro-3-(3-(4-chloro-3,5-dimethylphenoxy)propyl)-1H-indole-2-carboxylic acid, we applied a fragment-based approach to obtain new molecules that extended into the p1 pocket of the BH3 groove and then exhibited binding selectivity for the Mcl-1 over the Bcl-2 protein. After we deconstructed the 1H-indole-2-carboxylic acid from the parental molecule, a benzenesulfonyl was substituted at the 1-position to adopt a geometry preferred for accessing the p1 pocket according to the binding mode of the parental molecule identified by X-ray crystallography...
December 2, 2016: Archiv der Pharmazie
https://www.readbyqxmd.com/read/27910993/synthesis-and-full-characterization-of-an-iridium-b-h-activation-intermediate-of-the-monocarba-closo-dodecaborate-anion
#6
Yunjun Shen, Yani Pan, Jiyong Liu, Tosaporn Sattasathuchana, Kim K Baldridge, Simon Duttwyler
The preparation and full characterization of an iridium complex of the monocarba-closo-dodecaborate anion is reported. It was prepared by B-H bond activation using a tosyl amide directing group. Analysis by spectroscopic methods and X-ray crystallography revealed the presence a direct B-Ir interaction. The carborane acts as a B,N chelating ligand towards the Ir(Cp*)(solvent) fragment, resulting in a monomeric complex that is inert in solution and the solid state. Treatment with N-chlorosuccinimide resulted in selective monochlorination of the B-Ir position...
December 2, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27907874/synthesis-of-copper-and-zinc-2-pyridin-2-yl-imidazo-1-2-a-pyridine-complexes-and-their-potential-anticancer-activity
#7
Jean Dam, Zeenat Ismail, Taurai Kurebwa, Nadia Gangat, Leonie Harmse, Helder M Marques, Andreas Lemmerer, Moira L Bode, Charles B de Koning
A small library of novel copper and zinc imidazo[1,2-a]pyridine complexes have been synthesized. Their structures were confirmed by X-ray diffraction crystallography and a selection of these compounds was tested against five cancer cell lines originating from breast cancer (MCF-7 and MDA-MB-231), leukemia (K562 and HL-60) and colorectal cancer (HT-29). The imidazo[1,2-a]pyridines and their zinc complexes showed poor anticancer activity, while the copper complexes were active against the cancer cell lines with IC50 values comparable to and lower than camptothecin...
November 11, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27905149/scope-limitations-of-fmoc-chemistry-spps-based-approaches-to-the-total-synthesis-of-insulin-lispro-via-ester-insulin
#8
Stephen Kent, Balamurugan Dhayalan, Kalyaneswar Mandal, Nischay Rege, Michael Weiss, Simon Eitel, Thomas Meier, Ralph Schoenleber
We have systematically explored three approaches based on Fmoc chemistry SPPS for the total chemical synthesis of the key depsipeptide intermediate for the efficient total chemical synthesis of insulin. The approaches used were: stepwise Fmoc chemistry SPPS; the 'hybrid method', in which maximally-protected peptide segments made by Fmoc chemistry SPPS are condensed in solution; and, native chemical ligation using peptide-thioester segments generated by Fmoc chemistry SPPS. A key building block in all three approaches was a Glu[Oβ(Thr)] ester-linked dipeptide equipped with a set of orthogonal protecting groups compatible with Fmoc chemistry SPPS...
November 30, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27900844/cerium-catalyzed-hydrosilylation-of-acrylates-to-give-%C3%AE-silyl-esters
#9
Aradhana Pindwal, Smita Patnaik, William C Everett, Arkady Ellern, Theresa L Windus, Aaron D Sadow
The homoleptic organocerium complex Ce{C(SiHMe2 )3 }3 (1) reacts with B(C6 F5 )3 to produce the zwitterionic bis(alkyl) hydridoborato Ce{C(SiHMe2 )3 }2 HB(C6 F5 )3 (2). NMR and IR spectroscopy and X-ray crystallography indicate that each alkyl ligand contains two bridging Ce↼H-Si interactions in both 1 and 2. Compound 2 serves as a precatalyst for the hydrosilylation of acrylates to give α-silyl esters at room temperature with a turnover number of 2200.
November 30, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27900555/x-ray-crystallography-as-a-tool-to-determine-three-dimensional-structures-of-commercial-enzymes-subjected-to-treatment-in-pressurized-fluids
#10
REVIEW
Mirian Cristina Feiten, Marco Di Luccio, Karine F Santos, Débora de Oliveira, J Vladimir Oliveira
The study of enzyme function often involves a multi-disciplinary approach. Several techniques are documented in the literature towards determining secondary and tertiary structures of enzymes, and X-ray crystallography is the most explored technique for obtaining three-dimensional structures of proteins. Knowledge of three-dimensional structures is essential to understand reaction mechanisms at the atomic level. Additionally, structures can be used to modulate or improve functional activity of enzymes by the production of small molecules that act as substrates/cofactors or by engineering selected mutants with enhanced biological activity...
November 29, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27900513/synthesis-and-antimicrobial-evaluation-of-ester-linked-1-4-disubstituted-1-2-3-triazoles-with-a-furyl-thienyl-moiety
#11
C P Kaushik, Raj Luxmi, Dharmendra Singh, Ashwani Kumar
Twenty ester-linked 1,4-disubstituted 1,2,3-triazoles having a furyl/thienyl moiety have been synthesized from heteroaryl prop-2-yn-1-yl carboxylate and aromatic azides via a Cu(I) catalyzed 1,3-dipolar cycloaddition. All the synthesized compounds were characterized by FTIR, [Formula: see text]H NMR, [Formula: see text]C NMR spectroscopy and HRMS. Synthesized triazoles were tested in vitro for antimicrobial evaluation against Gram-negative bacteria-Escherichia coli, Enterobacter aerogenes and Klebsiella pneumoniae; Gram-positive bacteria-Staphylococcus aureus and two fungal strains-Candida albicans and Aspergillus niger, reflecting moderate to good activity...
November 29, 2016: Molecular Diversity
https://www.readbyqxmd.com/read/27900406/what-does-the-crystallography-of-stones-tell-us-about-their-formation
#12
REVIEW
Peter Rez
The mineral phase makes up most of the mass of a kidney stone. Minerals all come in the form of crystals that are regular arrangements of atoms or molecular groupings at the atomic scale, bounded macroscopically by well-defined crystal faces. Pathologic nephroliths are a polycrystalline aggregate of submicron crystals. Organic macromolecules clearly have an important role in either promoting or preventing aggregation and in altering the morphology of individual submicron crystals by influencing the surface energies of different faces...
November 29, 2016: Urolithiasis
https://www.readbyqxmd.com/read/27899601/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#13
Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J Oldfield, Maria Cristina Aspromonte, Norman E Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V Kajava, Lajos Kalmar, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B Roche, Edoardo Salladini, Eva Schad, Antoine Schramm, Beata Szabo, Agnes Tantos, Fiorella Tonello, Konstantinos D Tsirigos, Nevena Veljković, Salvador Ventura, Wim Vranken, Per Warholm, Vladimir N Uversky, A Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C E Tosatto
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27897427/structure-based-drug-design-of-mineralocorticoid-receptor-antagonists-to-explore-oxosteroid-receptor-selectivity
#14
Anneli Nordqvist, Gavin O'Mahony, Maria Fridén-Saxin, Marlene Fredenwall, Anders Hogner, Kenneth L Granberg, Anna Aagaard, Stefan Bäckström, Anders Gunnarsson, Tim Kaminski, Yafeng Xue, Anita Dellsén, Eva Hansson, Pia Hansson, Ida Ivarsson, Ulla Karlsson, Krister Bamberg, Majlis Hermansson, Jennie Georgsson, Bo Lindmark, Karl Edman
The mineralocorticoid receptor (MR) is a nuclear hormone receptor involved in regulation of body fluid and electrolyte homeostasis. In this study we explore selectivity triggers for a series of non-steroidal MR antagonists to improve selectivity over other members of the oxosteroid receptor family. A biaryl sulfonamide compound was identified in a high-throughput screening (HTS) campaign. The compound bound to MR with a pKi=6.6, but displayed poor selectivity over the glucocorticoid receptor (GR) and the progesterone receptor (PR)...
November 29, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27897362/unambiguous-determination-of-protein-arginine-ionization-states-in-solution-by-nmr-spectroscopy
#15
Yuichi Yoshimura, Nur Alia Oktaviani, Kento Yonezawa, Hironari Kamikubo, Frans A A Mulder
Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge-neutral are rare and potentially controversial. Herein, we present a (13) C-detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the (15) N(η) and (15) N(ϵ) chemical shifts of an arginine head group are correlated with that of the directly attached (13) C(ζ) ...
November 29, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27897281/platinum-ii-o-s-complexes-as-potential-metallodrugs-against-cisplatin-resistance
#16
Jana Hildebrandt, Norman Häfner, Helmar Görls, Daniel Kritsch, Giarita Ferraro, Matthias Dürst, Ingo B Runnebaum, Antonello Merlino, Wolfgang Weigand
We report on platinum(ii) complexes with different cinnamic acid derivatives as ligands with cytotoxic activity against Cisplatin resistant ovarian cancer cell line subcultures of SKOV3 and A2780. A typical mechanism of action for platinum(ii) complexes as Cisplatin itself is binding to the DNA and inducing double-strand breaks. We examined the biological behavior of these potential drugs with 9-methylguanine using NMR spectroscopic methods and their DNA damage potential including γH2AX-foci analyses. X-ray diffraction methods have been used to elucidate the molecular structures of the platinum(ii) complexes...
November 29, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27896733/3d-computational-modeling-of-proteins-using-sparse-paramagnetic-nmr-data
#17
Kala Bharath Pilla, Gottfried Otting, Thomas Huber
Computational modeling of proteins using evolutionary or de novo approaches offers rapid structural characterization, but often suffers from low success rates in generating high quality models comparable to the accuracy of structures observed in X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. A computational/experimental hybrid approach incorporating sparse experimental restraints in computational modeling algorithms drastically improves reliability and accuracy of 3D models. This chapter discusses the use of structural information obtained from various paramagnetic NMR measurements and demonstrates computational algorithms implementing pseudocontact shifts as restraints to determine the structure of proteins at atomic resolution...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896717/a-practical-approach-to-protein-crystallography
#18
Andrea Ilari, Carmelinda Savino
Macromolecular crystallography is a powerful tool for structural biology. The resolution of a protein crystal structure is becoming much easier than in the past, thanks to developments in computing, automation of crystallization techniques and high-flux synchrotron sources to collect diffraction datasets. The aim of this chapter is to provide practical procedures to determine a protein crystal structure, illustrating the new techniques, experimental methods, and software that have made protein crystallography a tool accessible to a larger scientific community...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895259/arene-guest-selectivity-and-pore-flexibility-in-a-metal-organic-framework-with-semi-fluorinated-channel-walls
#19
Rebecca Smith, Iñigo J Vitórica-Yrezábal, Adrian Hill, Lee Brammer
A metal-organic framework (MOF) with one-dimensional channels of approximately hexagonal cross-section [Ag2(O2CCF2CF2CO2)(TMP)] 1: (TMP =2,3,5,6-tetramethylpyrazine) has been synthesized with MeOH filling the channels in its as-synthesized form as [Ag2(O2CCF2CF2CO2)(TMP)]·n(MeOH) 1-MEOH: (n = 1.625 by X-ray crystallography). The two types of ligand connect columns of Ag(I) centres in an alternating manner, both around the channels and along their length, leading to an alternating arrangement of hydrocarbon (C-H) and fluorocarbon (C-F) groups lining the channel walls, with the former groups projecting further into the channel than the latter...
January 13, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/27895258/x-ray-crystallographic-insights-into-post-synthetic-metalation-products-in-a-metal-organic-framework
#20
Michael T Huxley, Campbell J Coghlan, Witold M Bloch, Alexandre Burgun, Christian J Doonan, Christopher J Sumby
Post-synthetic modification of metal-organic frameworks (MOFs) facilitates a strategic transformation of potentially inert frameworks into functionalized materials, tailoring them for specific applications. In particular, the post-synthetic incorporation of transition-metal complexes within MOFs, a process known as 'metalation', is a particularly promising avenue towards functionalizing MOFs. Herein, we describe the post-synthetic metalation of a microporous MOF with various transition-metal nitrates. The parent framework, 1: , contains free-nitrogen donor chelation sites, which readily coordinate metal complexes in a single-crystal to single-crystal transformation which, remarkably, can be readily monitored by X-ray crystallography...
January 13, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
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