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Protocol for Molecular Dynamics Simulations of Proteins

Featured protocol,  Authors: MNV Prasad Gajula
MNV Prasad GajulaAffiliation 1: Institute of Biotechnology, PJTSAU, Rajendra Nagar, Hyderabad, India
Affiliation 2: Bioclues.org, Kukatpally, Telangana, India
For correspondence: gajula.ibt@gmail.com
Bio-protocol author page: a3836
Anuj Kumar
Anuj KumarAffiliation: Bioinformatics center, Uttarakhand Council for Biotechnology,, Dehradun, India
Bio-protocol author page: a3837
 and Johny Ijaq
Johny IjaqAffiliation: Department of Zoology, Osmania University, Hyderabad, India
Bio-protocol author page: a3838
date: 12/5/2016, 130 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.2051.

Brief version appeared in BMC Genomics, Oct 2013
Molecular dynamics (MD) simulations have become one of the most important tools in understanding the behavior of bio-molecules on nanosecond to microsecond time scales. In this protocol, we provide a general approach and standard setup protocol for MD simulations by using the Gromacs MD suite.

Protocol for Molecular Dynamics Simulations of Proteins

Authors: MNV Prasad Gajula
MNV Prasad GajulaAffiliation 1: Institute of Biotechnology, PJTSAU, Rajendra Nagar, Hyderabad, India
Affiliation 2: Bioclues.org, Kukatpally, Telangana, India
For correspondence: gajula.ibt@gmail.com
Bio-protocol author page: a3836
Anuj Kumar
Anuj KumarAffiliation: Bioinformatics center, Uttarakhand Council for Biotechnology,, Dehradun, India
Bio-protocol author page: a3837
 and Johny Ijaq
Johny IjaqAffiliation: Department of Zoology, Osmania University, Hyderabad, India
Bio-protocol author page: a3838
date: 12/5/2016, 130 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.2051.

[Abstract] Molecular dynamics (MD) simulations have become one of the most important tools in understanding the behavior of bio-molecules on nanosecond to microsecond time scales. In this protocol, we provide a general approach and standard setup protocol for MD simulations by using the Gromacs MD suite.
Keywords: Molecular dynamics simulations, Conformational ...

Sequencing of Ebola Virus Genomes Using Nanopore Technology

Author: Thomas Hoenen
Thomas HoenenAffiliation: Friedrich-Loeffler-Institut, Greifswald – Isle of Riems, Germany
For correspondence: thomas.hoenen@fli.de
Bio-protocol author page: a3685
date: 11/5/2016, 304 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1998.

[Abstract] Sequencing of virus genomes during disease outbreaks can provide valuable information for diagnostics, epidemiology, and evaluation of potential countermeasures. However, particularly in remote areas logistical and technical challenges can be significant. Nanopore sequencing provides an alternative to classical Sanger and next-generation sequencing ...

Metabolite Profiling of Mature Arabidopsis thaliana Seeds Using Gas Chromatography-Mass Spectrometry (GC-MS)

Authors: Hagai Cohen
Hagai CohenAffiliation 1: Laboratory of Plant Science, Migal Galilee Technology Center, Kiryat Shmona, Israel
Affiliation 2: Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
For correspondence: Hagaic@Weizmann.ac.il
Bio-protocol author page: a3644
Ifat Matityahu
Ifat MatityahuAffiliation: Laboratory of Plant Science, Migal Galilee Technology Center, Kiryat Shmona, Israel
Bio-protocol author page: a3645
 and Rachel Amir
Rachel AmirAffiliation 1: Laboratory of Plant Science, Migal Galilee Technology Center, Kiryat Shmona, Israel
Affiliation 2: Tel-Hai College, Upper Galilee, Israel
For correspondence: Rachel@migal.org.il
Bio-protocol author page: a3646
date: 11/5/2016, 192 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1981.

[Abstract] Metabolite profiling using gas chromatography-mass spectrometry (GC-MS) permits the annotation and quantification of a relatively wide variety of metabolites, covering a wide range of biochemical groups of metabolites. Lisec et al. (2006) established a method for GC-MS profiling in plants. Based on this protocol, we provide here a detailed GC-MS-based ...

Chromosome Dosage Analysis in Plants Using Whole Genome Sequencing

Authors: Ek Han Tan
Ek Han TanAffiliation: Plant Biology Dept. and Genome Center, University of California, Davis, USA
Bio-protocol author page: a3267
Luca Comai
Luca ComaiAffiliation: Plant Biology Dept. and Genome Center, University of California, Davis, USA
Bio-protocol author page: a3268
 and Isabelle M. Henry
Isabelle M. HenryAffiliation: Plant Biology Dept. and Genome Center, University of California, Davis, USA
For correspondence: imhenry@ucdavis.edu
Bio-protocol author page: a3269
date: 7/5/2016, 672 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1854.

[Abstract] Relative chromosome dosage, i.e., increases or decreases in the number of copies of specific chromosome regions in one sample versus another, can be determined using aligned read-counts from Illumina sequencing (Henry et al., 2010). The following protocol was used to identify the different classes of aneuploids that result from uniparental genome elimination ...

Computational Identification of MicroRNA-targeted Nucleotide-Binding Site-Leucine-Rich Repeat Genes in Plants

Authors: Zhu-Qing Shao*
Zhu-Qing ShaoAffiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
Bio-protocol author page: a2675
Yan-Mei Zhang*
Yan-Mei ZhangAffiliation 1: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
Affiliation 2: Institute of Botany, Jiangsu Province & Chinese Academy of Science, Nanjing, China
Bio-protocol author page: a2676
Bin Wang
Bin WangAffiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
For correspondence: binwang@nju.edu.cn
Bio-protocol author page: a2677
 and Jian-Qun Chen
Jian-Qun ChenAffiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
For correspondence: chenjq@nju.edu.cn
Bio-protocol author page: a2678
 (*contributed equally to this work) date: 11/5/2015, 1188 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1637.

[Abstract] Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR, NBS for short) type disease resistance genes (Shao et al., 2014; Zhang et al., 2015). Proper regulation of these genes is important for normal growth of plants by reducing unnecessary fitness costs in the absence of pathogen infection. Recent studies have ...

Character-State Reconstruction to Infer Ancestral Protein-Protein Interaction Patterns

Authors: Florian Rümpler
Florian RümplerAffiliation: Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
Bio-protocol author page: a2486
Günter Theißen
Günter TheißenAffiliation: Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
Bio-protocol author page: a1560
 and Rainer Melzer
Rainer MelzerAffiliation 1: Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
Affiliation 2: School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
For correspondence: rainer.melzer@ucd.ie
Bio-protocol author page: a2487
date: 8/20/2015, 1505 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1566.

[Abstract] Protein-protein interactions are at the core of a plethora of developmental, physiological and biochemical processes. Consequently, insights into the origin and evolutionary dynamics of protein-protein interactions may provide information on the constraints and dynamics of specific biomolecular circuits and their impact on the organismal phenotype. ...

Protocol for the Generation of a Transcription Factor Open Reading Frame Collection (TFome)

Authors: John Gray*
John GrayAffiliation: Department of Biological Sciences, University of Toledo, Ohio, USA
For correspondence: john.gray5@utoledo.edu
Bio-protocol author page: a2417
Brett Burdo*
Brett BurdoAffiliation: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, USA
Bio-protocol author page: a2418
Mary P. Goetting-Minesky
Mary P. Goetting-MineskyAffiliation: Department of Biological Sciences, University of Toledo, Ohio, USA
Bio-protocol author page: a2419
Bettina Wittler
Bettina WittlerAffiliation: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, USA
Bio-protocol author page: a2420
Matthew Hunt
Matthew HuntAffiliation: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, USA
Bio-protocol author page: a2421
Tai Li
Tai LiAffiliation: Department of Biological Sciences, University of Toledo, Ohio, USA
Bio-protocol author page: a2422
David Velliquette
David VelliquetteAffiliation: Department of Biological Sciences, University of Toledo, Ohio, USA
Bio-protocol author page: a2423
Julie Thomas
Julie ThomasAffiliation: Department of Biological Sciences, University of Toledo, Ohio, USA
Bio-protocol author page: a2424
Tina Agarwal
Tina AgarwalAffiliation: Department of Biological Sciences, University of Toledo, Ohio, USA
Bio-protocol author page: a2425
Kasey Key
Kasey KeyAffiliation: Department of Biological Sciences, University of Toledo, Ohio, USA
Bio-protocol author page: a2426
Irene Gentzel
Irene GentzelAffiliation: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, USA
Bio-protocol author page: a2427
Michael dos Santos Brito
Michael dos Santos BritoAffiliation: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, USA
Bio-protocol author page: a2428
Maria Katherine Mejía-Guerra
Maria Katherine Mejía-GuerraAffiliation: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, USA
Bio-protocol author page: a2429
Layne N. Connolly
Layne N. ConnollyAffiliation: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, USA
Bio-protocol author page: a2430
Dalya Qaisi
Dalya QaisiAffiliation: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, USA
Bio-protocol author page: a2431
Wei Li
Wei LiAffiliation 1: Department of Molecular Genetics, The Ohio State University, Columbus, USA
Affiliation 2: Department of Physiology and Cell Biology, The Heart and Lung Research Institute, The Ohio State University, Columbus, USA
Bio-protocol author page: a2432
Maria I. Casas
Maria I. CasasAffiliation: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, USA
Bio-protocol author page: a2433
Andrea I. Doseff
Andrea I. DoseffAffiliation 1: Department of Molecular Genetics, The Ohio State University, Columbus, USA
Affiliation 2: Department of Physiology and Cell Biology, The Heart and Lung Research Institute, The Ohio State University, Columbus, USA
Bio-protocol author page: a2434
 and Erich Grotewold
Erich GrotewoldAffiliation 1: Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbu, USA
Affiliation 2: Department of Molecular Genetics, The Ohio State University, Columbus, USA
Bio-protocol author page: a2435
 (*contributed equally to this work) date: 8/5/2015, 1483 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1547.

[Abstract] The construction of a physical collection of open reading frames (ORFeomes) for genes of any model organism is a useful tool for the exploration of gene function, gene regulation, and protein-protein interaction. Here we describe in detail a protocol that has been used to develop the first collection of transcription factor (TF) and co-regulator (CR) ...

A Phosphopeptide Purification Protocol for the Moss Physcomitrella paten

Authors: Xiaoqin Wang
Xiaoqin WangAffiliation 1: Beijing University of Agriculture, Beijing, China
Affiliation 2: College of Life Sciences, Capital Normal University, Beijing, China
For correspondence: wxqtycn@gmail.com
Bio-protocol author page: a2367
 and Yikun He
Yikun HeAffiliation: College of Life Sciences, Capital Normal University, Beijing, China
For correspondence: yhe@cnu.edu.cn
Bio-protocol author page: a2368
date: 7/20/2015, 1230 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1527.

[Abstract] Protein phosphorylation is one of the most common post-translational modifications in eukaryotic cells and plays a critical role in a vast array of cellular processes. Efficient methods of protein extraction and phosphopeptide purification are required to ensure the detection of high quality of proteins. In our hands, phenol extraction of proteins ...

Large-scale Phenotypic Profiling of Gene Deletion Mutants in Candida glabrata

Authors: Fabian Istel*
Fabian IstelAffiliation: Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University Vienna, Vienna, Austria
Bio-protocol author page: a2372
Tobias Schwarzmüller*
Tobias SchwarzmüllerAffiliation: Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University Vienna, Vienna, Austria
Bio-protocol author page: a2373
Michael Tscherner
Michael TschernerAffiliation: Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University Vienna, Vienna, Austria
Bio-protocol author page: a929
 and Karl Kuchler
Karl KuchlerAffiliation: Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University Vienna, Vienna, Austria
For correspondence: karl.kuchler@meduniwien.ac.at
Bio-protocol author page: a496
 (*contributed equally to this work) date: 7/20/2015, 1439 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1530.

[Abstract] Here, we describe a method enabling the phenotypic profiling of genome-scale deletion collections of fungal mutants to detect phenotypes for various stress conditions. These stress conditions include among many others antifungal drug susceptibility, temperature-induced and osmotic as well as heavy metal or oxidative stress. The protocol was extensively ...

Human, Bacterial and Fungal Amplicon Collection and Processing for Sequencing

Author: Julia Oh
Julia OhAffiliation: National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
For correspondence: jsoh@alumni.stanford.edu
Bio-protocol author page: a2228
date: 5/20/2015, 1724 views, 2 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.1477.

[Abstract] Sequencing taxonomic marker genes is a powerful tool to interrogate the composition of microbial communities. For example, bacterial and fungal community composition can be evaluated in parallel using the 16S ribosomal RNA gene for bacteria or the internal transcribed spacer region in fungi. These are conserved regions that are universal to a taxonomic ...
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Nuclear Extraction from Arabidopsis thaliana

Authors: Fang Xu
Fang XuAffiliation: Department of Botany and Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
For correspondence: xufang@mail.ubc.ca
Bio-protocol author page: a188
 and Charles Copeland
Charles CopelandAffiliation: Department of Botany and Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
Bio-protocol author page: a189
date: 12/20/2012, 9669 views, 5 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.306.

[Abstract] This protocol is to isolate nuclei from Arabidopsis cells. They can be further used for other experiments, such as nuclear protein detection, nuclear protein immunoprecipitation and so on....

Illumina Sequencing Library Construction from ChIP DNA

Author: Wei Zheng
Wei ZhengAffiliation: Keck Biotech Services, Yale University, New Haven, USA
For correspondence: wei.zheng.madison@gmail.com
Bio-protocol author page: a10
date: 2/20/2012, 9219 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.91.

[Abstract] The Illumina sequencing platform is very popular among next-generation sequencing platforms. However, the DNA sequencing library construction kit provided by Illumina is considerably expensive. The protocol described here can be used to construct high-quality sequencing libraries from chromatin immunoprecipitated ...

[Bio101] Protein-ligand Binding Assay by Liquid Chromatography-Mass Spectrometry

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 8/20/2011, 8867 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.124.

[Abstract] Protein-small molecule binding coefficients are determined by quantitative LC-MS in this method. Traditional biochemical plot is consequently used to set up the binding curve between a known protein and a small molecule (<1000 Da) to determine the affinity constant (Kd) and the stoichiometry (Bmax)....

[Bio101] Affinity Purification of Yeast Protein-interacting Metabolites for ESI-MS Analysis

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 4/20/2011, 8503 views, 5 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.61.

[Abstract] The method described here can be used to discover in vivo protein-metabolite interactions. Metabolite-protein complexes are purified from yeast cell lysates by an affinity tag that recognizes the protein of interest. The protein-bound metabolites are extracted for identification by mass spectrometry, ...

[Bio101] Rabbit IgG Conjugation to Dynabeads

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 5/5/2011, 8285 views, 1 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.63.

[Abstract] This method couples rabbit IgG (or any other proteins serve as affinity reagent) to the surface of magnetic beads (Brand name: Dynabeads). The amine and thiol groups of amino acid residues on the protein are covalently linked with the epoxy group on Dynabeads. The coupled IgG beads can be stored at ...

[Bio101] In-Solution Digestion Of Purified Yeast Protein For LC-MS

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford , USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 4/20/2011, 7289 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.62.

[Abstract] This method describes the preparation of total yeast protein extract for mass spectrometry analysis. The protein extract is digested by trypsin in a solution with strong denaturants. The digested sample is dried and re-constituted in a mixture compatible with HPLC separation. Samples of isobaric labels ...

Quantitative Methylation Specific PCR (qMSP)

Authors: Triantafillos Liloglou
Triantafillos LiloglouAffiliation: Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
For correspondence: tliloglo@liv.ac.uk
Bio-protocol author page: a778
 and Georgios Nikolaidis
Georgios NikolaidisAffiliation: Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
Bio-protocol author page: a779
date: 8/20/2013, 7242 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.871.

[Abstract] Detection of low copies of methylated DNA targets in clinical specimens is challenging. The quantitative Methylation-Specific PCR (qMSP) assays were designed to specifically amplify bisulphite-converted methylated DNA target sequences in the presence of an excess of unmethylated counterpart sequences. ...

Gene Networks Based on the Graphical Gaussian Model

Author: Shisong Ma
Shisong MaAffiliation: Department of Plant Biology & Genome Center, University of California, Davis, USA
For correspondence: sma@ucdavis.edu
Bio-protocol author page: a23
date: 2/20/2012, 5629 views, 1 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.119.

[Abstract] This protocol describes how to build a gene network based on the graphical Gaussian model (GGM) from large scale microarray data. GGM uses partial correlation coefficient (pcor) to infer co-expression relationship between genes. Compared to the traditional Pearson’ correlation coefficient, partial correlation ...

Probing Yeast Protein Microarrays for Protein-protein Interactions Using V5-epitope Tagged Fusion Protein Probes

Authors: Joseph Fasolo
Joseph FasoloAffiliation: Department of Genetics, Stanford University, Stanford, USA
Bio-protocol author page: a22
 and Michael Snyder
Michael SnyderAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: mpsnyder@stanford.edu
Bio-protocol author page: a1789
date: 3/5/2012, 5521 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.123.

[Abstract] Protein microarray is probably the only technique currently available for systematic investigation of protein-protein interactions. This protocol describes an optimized method to probe yeast protein microarrays for protein-protein interactions using purified V5-epitope tagged fusion protein. It should ...

Construction and Screening of a Transposon Insertion Library of Yersinia enterocolitica (YeO3-R1)

Authors: Maria Pajunen
Maria PajunenAffiliation: Department of Biosciences, Division of Biochemistry and Biotechnology, University of Helsinki, Helsinki, Finland
Bio-protocol author page: a79
Elise Pinta
Elise PintaAffiliation: Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
Bio-protocol author page: a80
 and Mikael Skurnik
Mikael SkurnikAffiliation: Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland
For correspondence: mikael.skurnik@helsinki.fi
Bio-protocol author page: a78
date: 8/5/2012, 5212 views, 0 Q&A, How to cite
DOI: https://doi.org/10.21769/BioProtoc.246.

[Abstract] The Mu-transposon system is one of the best characterized transposition systems. Under minimal in vitro set-up, Mu transposition requires only a simple reaction buffer, MuA transposase protein, mini-Mu transposon DNA (donor) and target DNA. The reaction proceeds via initial assembly of the transposition ...
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