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Determining protein structure using the distance geometry program APA
1999
Computers and Chemistry
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APA is a computer program, written in C, designed to determine the three-dimensional structure of proteins using distance geometry. ...
In order to compare with Havel's DG-II distance geometry program, the sampling and convergence properties were tested on Havel's 10 data sets. ...
Robert Reams was supported as a postdoctoral scholar by the Center for Computational Sciences, University of Kentucky. ...
doi:10.1016/s0097-8485(99)00003-0
fatcat:qeh2ujq5orbjtns4sq7poru5ai
New Trends in Protein Nanocrystallography Based On LB Nanotemplate, Cell Free Expression, SNAP APA and Montecarlo: A Review
2014
Journal of Microbial & Biochemical Technology
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A review of the emerging trends and perspectives of Protein Nanocrystallography is here presented at the intersection of advances in nanotechnology (Langmuir-Blodgett and Anodic Porous Allumina), proteomics ...
, human kinase, laccase and many other proteins. ...
User in this case will construct structures of Protein crystals using Geant4 [24] and will compare MC simulation of LB vs Classical crystals basing on what we have determined down to the atomic scale ...
doi:10.4172/1948-5948.1000170
fatcat:jldohegf4rh55emagk5hkklfue
Molecular modeling studies of HIV-1 reverse transcriptase nonnucleoside inhibitors: Total energy of complexation as a predictor of drug placement and activity
1995
Protein Science
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In the correct site, these binding energies correlate with EC" values determined for all three inhibitors in our laboratory. ...
In general, the protein is energetically more stable and the drug less stable in their complexes as compared to the reactant conformations. ...
imply endorsement by the US government. ...
doi:10.1002/pro.5560041026
pmid:8535257
pmcid:PMC2142988
fatcat:c4u7xfmmynezbijd5bhzexf55e
Protein Crystallization by Anodic Porous Alumina (APA) Template: The Example of Hen Egg White Lysozyme (HEWL)
2015
NanoWorld Journal
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The APA nanotemplate was prepared on the glass substrate for the hen egg white lysozyme (HEWL) crystal growth. ...
phenomenon and shed light on the APA-induced nanocrystallography. ...
The phase problem was solved using the molecular replacement method, using the software package CNS and the threedimensional structures were determined from the electrondensity map, using the software ...
doi:10.17756/nwj.2015-006
fatcat:7f4ainvx5zg7zipcyyi2itlpiy
The disulfide-coupled folding pathway of apamin as derived from diselenide-quenched analogs and intermediates
1999
Protein Science
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Thus, selenocysteine can be used as a new device to generate productive and nonproductive folding intermediates of peptides and proteins. ...
Refolding experiments clearly revealed that the redox potential of selenocysteine prevails over the sequence encoded structural information for proper folding of apamin. ...
NOEs-derived distance constraints were then used to generated the solution structures of wt-apamin and of its Sec-containing analogs from distance geometry refined by molecular dynamicssimulated annealing ...
doi:10.1110/ps.8.8.1605
pmid:10452604
pmcid:PMC2144427
fatcat:l4c5avirmje35iuiwpawtyvada
Molecular modeling of HIV-1 reverse transcriptase drug-resistant mutant strains: implications for the mechanism of polymerase action
1997
Protein Engineering Design & Selection
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In addition, the level of activity was related to the measured distance between the primer grip and dNTP binding regions of the protein. ...
from a subset of the protein surrounding the binding pocket region. ...
imply endorsement by the US Government. ...
doi:10.1093/protein/10.12.1379
pmid:9542999
fatcat:edsko52c2vemxfrjxipwxekjie
Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor α-APA R 95845 at 2.8 å resolution
1995
Structure
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Acknowledgements: We thank P Van Daele for synthesizing the dibrominated derivative of ox-APA R 95845 for these studies, D Rodgers and SC Harrison for providing the unliganded HIV-1 RT coordinates prior ...
Structure determination The crystal structure of the HIV-I RT/a-APA complex was determined using the molecular replacement (MR) method as implemented in the program X-PLOR [22] . ...
The location of ot-APA was determined using the difference Fourier method. ...
doi:10.1016/s0969-2126(01)00168-x
pmid:7542140
fatcat:567644vlgza5zfbbmi2gfbnjzm
Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d
2005
Nucleic Acids Research
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Eight crystal structures of five Sac7d mutant-DNA complexes have been analyzed. ...
proteins. ...
ACKNOWLEDGEMENTS This research was supported by grants from Academia Sinica, the National Research Program for Genomic Medicine (NRPGM) and the National Science Council (NSC) for X-ray Core (NSC-93-3112 ...
doi:10.1093/nar/gki191
pmid:15653643
pmcid:PMC546169
fatcat:sheash53w5hpvl3fnfdgytotdm
Steered Molecular Dynamics Simulation on the Binding of NNRTI to HIV-1 RT
2003
Biophysical Journal
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The binding and unbinding processes of a-APA, an NNRTI, have been studied using nanosecond conventional molecular dynamics and steered molecular dynamics simulations. ...
The simulation results show that the unbinding process of a-APA consists of three phases based on the position of a-APA in relation to the entrance of the binding pocket. ...
The authors thank Dr. Helmut Grubmüller for his kindness in offering the EGO program. ...
doi:10.1016/s0006-3495(03)75088-7
pmid:12770866
pmcid:PMC1302942
fatcat:2scofhujcfa2pdswb7hqornb7e
Model building of disulfide bonds in proteins with known three-dimensional structure
1988
Protein Engineering Design & Selection
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ITo whom correspondence should be addressed As an aid in the selection of sites in a protein where a disulfide bond might be engineered, a computer program has been developed. ...
Model building of disulfide bonds in proteins with known threedimensional structure. %22Protein Engineering%2C Design and Selection%22, 2(2). ...
Acknowledgements We thank Dr W.Bode for making available the nagarse-eglin coordinates prior to publication. We thank Profs Jan Drenth and Wim HoI for stimulating discussions. ...
doi:10.1093/protein/2.2.119
pmid:3244694
fatcat:juess742r5gwxjfc5x3ohnh62a
Asteropine A, a Sialidase-Inhibiting Conotoxin-like Peptide from the Marine Sponge Asteropus simplex
2006
Chemistry and Biology
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The solution structure of APA as determined by NMR belongs to the four-loop class of cystine knots similar to those of some conotoxins and spider toxins. ...
Here we report the discovery of asteropine A (APA), a cystine knot to be isolated from marine sponges. ...
Turbyville, National Cancer Institute at Frederick, for reading the manuscript. We thank Professor Yasuo Suzuki, The University of Shizuoka, for a generous gift of the influenza virus. ...
doi:10.1016/j.chembiol.2006.05.010
pmid:16793514
fatcat:ncbrapdo2rfhpf7euy5lhwmxxy
Minimal Molecular Determinants of Substrates for Recognition by the Intestinal Peptide Transporter
1998
Journal of Biological Chemistry
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By employing computational analysis of possible substrate conformations in combination with transport assays using transgenic yeast cells and Xenopus laevis oocytes expressing PEPT1, the minimal structural ...
requirements for substrate binding and transport were determined. ...
Hediger for providing the cDNA of nSGLT1. ...
doi:10.1074/jbc.273.36.23211
pmid:9722551
fatcat:xf37zf5kv5hr7epbj63pisazwi
Structural Insights into Central Hypertension Regulation by Human Aminopeptidase A
2013
Journal of Biological Chemistry
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Results: We determined the crystal structures of APA complexed with different ligands and calcium. ...
Here, we determined the crystal structures of human APA and its complexes with different ligands and identified a calcium-binding site in the S1 pocket of APA. ...
Third, the geometry of the coordinated calcium is octahedral, consistent with the geometry for calcium coordination in other calcium-binding proteins (39, 40) . ...
doi:10.1074/jbc.m113.494955
pmid:23888046
pmcid:PMC3757224
fatcat:l4rtm3kpkndttobtkj65cpikca
Design and tuning of ionic liquid–based HNO donor through intramolecular hydrogen bond for efficient inhibition of tumor growth
2020
Science Advances
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Here, a series of ILs are developed using biocompatible ionic components, which realizes absorption of gaseous NO to yield IL-NONOates. ...
However, the tunability is limited to screen ionic components, and none realizes the kinetic tuning of drug release, which is a key challenge in the design of IL drugs. ...
The geometry optimization of linear structure and hydrogen bond stabilized structure and energy gap between them were showed in Fig. 2D . ...
doi:10.1126/sciadv.abb7788
pmid:33158861
pmcid:PMC7673712
fatcat:5rwlqhbnqna6lcy4ppd3667whi
The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations
1996
European Biophysics Journal
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Thus, the structural zinc ion can be used as a sensitive test of methods trying to model the surrounding medium in quantum chemical computations. ...
The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations Ryde, Ulf Link to publication Citation for published version (APA): Ryde ...
The protein coordinates were courteously provided by Eila Cedergren-Zeppezauer. The author is thankful to Gunnar Karlström and Björn O. Roos for fruitful discussions. ...
doi:10.1007/bf00205102
fatcat:gdo2gssfhzf3vhtzc2izjzyxau
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