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Determining protein structure using the distance geometry program APA

R Reams, G Chatham, W Glunt, D McDonald, T Hayden
1999 Computers and Chemistry  
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

Eugenia Pechkova
2014 Journal of Microbial & Biochemical Technology  
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

Marilyn B. Kroeger Smith, Stephen H. Hughes, Paul L. Boyer, Christopher J. Michejda, Carol A. Rouzer, Lisa A. Taneyhill, Richard H. Smith, Nathan A. Smith, Paul A.J. Janssen, Henri Moereels, Luc Koymans, Edward Arnold (+3 others)
1995 Protein Science  
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)

Eugenia Pechkova, Nicola Luigi Bragazzi, Claudio Nicolini
2015 NanoWorld Journal  
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

Stefano Pegoraro, Stella Fiori, Jörg Cramer, Sabine Rudolph-Böhner, Luis Moroder
1999 Protein Science  
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

M. B. Kroeger Smith, C. J. Michejda, S. H. Hughes, P. L. Boyer, P. A. Janssen, K. Andries, R. W. Buckheit, R. H. Smith
1997 Protein Engineering Design & Selection  
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

J Ding, K Das, C Tantillo, W Zhang, AD Clark, Jr, S Jessen, X Lu, Y Hsiou, A Jacobo-Molina, K Andries, R Pauwels, H Moereels (+7 others)
1995 Structure  
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

C.-Y. Chen
2005 Nucleic Acids Research  
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

Lingling Shen, Jianhua Shen, Xiaomin Luo, Feng Cheng, Yechun Xu, Kaixian Chen, Edward Arnold, Jianping Ding, Hualiang Jiang
2003 Biophysical Journal  
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

Bart Hazes, Bauke W. Dijkstra
1988 Protein Engineering Design & Selection  
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

Kentaro Takada, Toshiyuki Hamada, Hiroshi Hirota, Yoichi Nakao, Shigeki Matsunaga, Rob W.M. van Soest, Nobuhiro Fusetani
2006 Chemistry and Biology  
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

Frank Döring, Jutta Will, Salah Amasheh, Wolfgang Clauss, Hubertus Ahlbrecht, Hannelore Daniel
1998 Journal of Biological Chemistry  
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

Yang Yang, Chang Liu, Yi-Lun Lin, Fang Li
2013 Journal of Biological Chemistry  
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

Xiaoyu Lv, Kaihong Chen, Guiling Shi, Wenjun Lin, Hongzhen Bai, Haoran Li, Guping Tang, Congmin Wang
2020 Science Advances  
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

Ulf Ryde
1996 European Biophysics Journal  
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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