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Prediction of Interacting Single-Stranded RNA Bases by Protein-Binding Patterns
2008
Journal of Molecular Biology
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These are recognized by a new classification methodology which is based on spatial multiple alignment. ...
The contacts are often with the unpaired nucleic acid bases, while the direct contacts with the phosphate moieties of the backbone, which point towards the bulk solution can be rare 15 . ...
As expected, the prediction was made based on four 3D consensus patterns of homologous proteins (1wrq, 1wmq), the chaining of which constituted the top ranking solution. ...
doi:10.1016/j.jmb.2008.03.043
pmid:18452949
pmcid:PMC2429989
fatcat:vsfv4eb7erbfvh75xnk253ua2e
Observation of metal ion dependent packing structures and magnetic behaviors of metal-bis-1, 2-dithiolene complexes
2012
Dalton Transactions
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Complex 1 shows the magnetic characteristics of a low-dimensional antiferromagnetic coupling spin system with a spin-Peierls-type transition around 7 K, and complex 2 exhibits diamagnetism over the temperature ...
Theoretical analyses, based on the calculations for the charge density distributions of [Pt(mnt) 2 ] − and [Pd(mnt) 2 ] − anions and the magnetic exchange constants within the anion spin chains, addressed ...
In this case, one type of spin dimer in 1 (regular spin chain) and two types of spin dimers in 2 (irregular spin chain) were concerned. ...
doi:10.1039/c1dt11477h
pmid:22237662
fatcat:j2mfr7y2zvhdbe2e4gr6ob63z4
Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta -branched amino acids
1999
Proceedings of the National Academy of Sciences of the United States of America
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In this model, steric hindrance is expected for NRTIs with -or L-ring configurations, as with the enantiomer of 3TC that is used in therapy. ...
However, comparison of crystal structures of M184I mutant and wild-type HIV-1 RT with and without DNA reveals repositioning of the template-primer in the M184I͞DNA binary complex and other smaller changes ...
We thank Aaron Shatkin for useful suggestions on the manuscript, Pat Clark for help in protein production, and Yu Hsiou, Karen Lentz, Chris Tantillo ...
doi:10.1073/pnas.96.18.10027
pmid:10468556
pmcid:PMC17836
fatcat:qti7yjmsajextkizr5yb4bv624
Development of small molecules designed to modulate protein–protein interactions
2006
Journal of Computer-Aided Molecular Design
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We describe a general approach based on the "privileged-structure hypothesis" [Che, Ph.D. ...
Developing small molecules that modulate proteinprotein interactions is challenging, owing to the large size of protein-complex interface, the lack of welldefined binding pockets, etc. ...
In helices, the side chains project outward into solution, although they are tilted toward the amino end of the helix, and need not interfere with the helical backbone. ...
doi:10.1007/s10822-006-9040-8
pmid:16622794
fatcat:s2s22l6g5jhj7i44ykehd3ax7e
Solutions for Torque and Speed Measurement on Electric Machine Controllers Test Benches
2021
Revista Elektrón
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ACKNOWLEDGMENT This work has received funding from the University of Buenos Aires with funds from the subsidy UBACYT 20620170100006BA ...
To achieve this, a design was made in our laboratory based on low-cost flexible couplings with an elastomer stars [22] . ...
In slip-ring based transducers the brush wear must be checked and cleanliness is essential to avoid scratches on the silver rings. ...
doi:10.37537/rev.elektron.5.1.131.2021
fatcat:zrzl64x2lbhetgz6weujjnlnva
Identification of the catalytic glutamate in the E1 component of human pyruvate dehydrogenase
1998
FEBS Letters
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The pyruvate dehydrogenase complex catalyzes the conversion of pyruvate to acetyl-CoA. ...
Eukaryotic E1 has an K K P L L P structure and the conserved Glu VW of the L L-subunit was identified as a possible catalytic residue by sequence alignment. ...
Georg Sprenger (Institut fu ë r Biotechnologie 1 des Forschungszentrums Ju ë lich, Germany) for details of the alignment between transketolase, DXP synthase and E1. ...
doi:10.1016/s0014-5793(98)01249-6
pmid:9824306
fatcat:zhwy4ybz55fa3ogk3xavukuo6u
Structure-based Inhibitor Design for an Enzyme That Binds Different Steroids
2006
Journal of Biological Chemistry
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The crystal structure of the type 5 enzyme in complex with NADP and such a novel inhibitor, EM1404, was determined to a resolution of 1.30 Å . ...
Several chemicals were synthesized and tested for their ability to inhibit this enzyme, and a series of estradiol derivatives bearing a lactone on the D-ring were found to inhibit its activity efficiently ...
Structural Features of 17-HSD Type 5 Pertinent to Inhibitor Design-A structure-based sequence alignment of several AKR family members revealed that only human 17-HSD5 has a serine at position 118, whereas ...
doi:10.1074/jbc.m606784200
pmid:17166832
fatcat:alajgtj73raebf2nz2shdof36e
Crystallographic Structure of the Nuclease Domain of 3′hExo, a DEDDh Family Member, Bound to rAMP
2004
Journal of Molecular Biology
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The bound rAMP is positioned within a deep active-site pocket, with its purine ring close-packed with the hydrophobic F185 and L189 side-chains and its sugar 2′-OH and 3′-OH groups hydrogen bonded to backbone ...
We have determined the structure of the nuclease domain (Nuc) of 3′hExo complexed with rAMP in the presence of Mg 2+ at 1.6 Å resolution. ...
One face of the purine ring of rAMP is involved in strong stacking with two hydrophobic residues, F185 and L189, in the Nuc complex (Figure 3(A) ), with their counterparts in ERI-1 being F205 and F209 ...
doi:10.1016/j.jmb.2004.08.055
pmid:15451662
pmcid:PMC4692376
fatcat:2gfrbbgi35gktkvbtbcynozneu
New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins
2015
Scientific Reports
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E3 ubiquitin ligases can be classified into two main categories: RING-type and HECT (homologous with E6-associated protein C-terminus)-type, which differ in their three-dimensional structures and mechanisms ...
RNA binding influences RC3H2 ubiquitination activity, but has differential effects on polyubiquitination when RC3H2 is paired with various E2 enzymes. ...
Yi Sheng (York University, Toronto) for her critical comments on the manuscript, Dr. Rachel Harding (University of Toronto) for proof-reading. ...
doi:10.1038/srep15660
pmid:26489670
pmcid:PMC4614863
fatcat:jpukvt5fhrcd3b5vn56xmm4eny
Enzyme-mimetic self-catalyzed polymerization of polypeptide helices
2019
Nature Communications
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Such folding-dependent catalytic behaviors, however, are seldom mechanistically explored with reduced structural complexity. ...
A two-stage, Michaelis-Menten-type kinetic model is proposed by considering the binding and reaction between the propagating helical chains and the monomers, and is successfully utilized to predict the ...
complex M i *−M, with an adsorption rate constant k on and a desorption rate constant k off ; subsequently, the attack of the active end of the helical chain on the bound monomer triggers a ring-opening ...
doi:10.1038/s41467-019-13502-w
pmid:31784526
pmcid:PMC6884638
fatcat:sbyug5jc6ncbvjub2t7ox3zyx4
New antibacterial agents: Hybrid bioisoster derivatives as potential E. coli FabH inhibitors
2016
Bioorganic & Medicinal Chemistry Letters
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In this regard, we propose the design, synthesis and biological evaluation of hybrid sulfonylhydrazone bioisosters/furoxans with potential antibacterial (Escherichia coli) activity. ...
The most active compound of the series, (E)-3-methyl-4-((2-tosylhydrazono)methyl)-1,2,5oxadiazole 2-oxide, with a MIC = 0.36 lM, was not cytotoxic when tested on Vero cells (IC 50 >100 lM). ...
Additionally, the applied strategy was based on the alignment of prototype B and the proposed scaffold, obtained through Computer Aided Drug Design (CADD) (Supplementary information). ...
doi:10.1016/j.bmcl.2016.06.089
pmid:27426865
fatcat:txvcjakvyzb7borh2dorcy2i4a
Active Angular Alignment of Gauge Blocks in Double-Ended Interferometers
2013
Sensors
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The system combines low-coherence interferometry and laser interferometry, where the first identifies the gauge block sides position and the second one measures the gauge block length itself. ...
This paper presents a method implemented in a system for automatic contactless calibration of gauge blocks designed at ISI ASCR. ...
The principle of the measurement is based on low-coherence interferometry taking advantage of low-coherence properties of the broadband light source. ...
doi:10.3390/s131013090
pmid:24084107
pmcid:PMC3859052
fatcat:6qyyjuqa4nftpo6hesq7wqbuem
The v-myc-induced Q83 Lipocalin Is a Siderocalin
2010
Journal of Biological Chemistry
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In addition, we also present the solution structure of Q83 in complex with intact enterobactin and a detailed analysis of the Q83 binding mode, including mutagenesis of the critical residues involved in ...
The Q83 lipocalin was originally identified based on its overexpression in quail embryo fibroblasts transformed by the v-myc oncogene. ...
3 seems to be stabilized bystacking with the Trp 62 side chain and cation-interaction with the side chain of Lys 83 .Enterobactin Binding Mode-The solution structure of the Q83/[Ga III (Ent)] 3Ϫ complex ...
doi:10.1074/jbc.m110.123331
pmid:20826777
pmcid:PMC3009892
fatcat:limejizhkrhelatky4tbd6ysay
Modern High Resolution NMR for the Study of Structure, Dynamics and Interactions of Biological Macromolecules
2006
Zeitschrift fur physikalische Chemie (Munchen. 1991)
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The main emphasis of the second part is on molecular interactions. ...
Solution NMR / Structure / Dynamics / Interactions High resolution liquid state nuclear magnetic resonance spectroscopy (NMR) is a powerful technique for in vitro studies of structure and dynamics of soluble ...
Holger Schmidt kindly provided the NMR spectra and structure of the peptide-human Hck SH3 complex shown in Fig. 8 ...
doi:10.1524/zpch.2006.220.5.567
fatcat:prg6zjxcmjgotb4cx4njgintua
Structural Basis of Inhibition of the Pioneer Transcription Factor NF-Y by Suramin
2020
Cells
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, that may represent a promising starting point for rational design of more specific and potent inhibitors with potential therapeutic applications. ...
With virtual-screening docking simulations on a library of pharmacologically active compounds, we identified suramin as a potential NF-Y inhibitor. ...
Based on these data, we designed a double-dependent binding site model where the binding of suramin to NF-Yd forms a ligand-receptor complex, which in turn generates a binding surface for a second NF-Yd ...
doi:10.3390/cells9112370
pmid:33138093
pmcid:PMC7692634
fatcat:5joinayxird7bboubupwpf2ycu
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