A 4-string tangle analysis of DNA-protein complexes based on difference topology

2015 ◽  
Vol 24 (11) ◽  
pp. 1550056 ◽  
Author(s):  
Soojeong Kim ◽  
Isabel K. Darcy
Keyword(s):  
Dna Sequences ◽  
Protein Complex ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Dna Complexes ◽  
Circular Dna ◽  
Biologically Relevant ◽  
Dimensional Ball ◽  
Dna Complex ◽  
Tangle Model

An n-string tangle is a three-dimensional ball with n-strings properly embedded in it. In the late 1980s, Ernst and Sumners introduced a tangle model for protein-DNA complexes. The protein is modeled by a three-dimensional ball and the protein-bound DNA is modeled by strings embedded inside the ball. Originally the tangle model was applied to proteins such as Tn3 resolvase which binds two DNA segments. This protein breaks and rejoins two DNA segments and can create knotted DNA. A 2-string tangle model can be used for this complex. More recently, Pathania, Jayaram and Harshey determined that the topological structure of DNA within a Mu protein complex consists of three DNA segments containing five crossings. Since Mu binds DNA sequences at three sites, this Mu protein-DNA complex can be modeled by a 3-string tangle. Darcy, Leucke and Vazquez analyzed Pathania et al.'s experimental results by using 3-string tangle analysis. There are protein-DNA complexes that involve four or more DNA sites. When a protein binds circular DNA at four sites, a protein-DNA complex can be modeled by a 4-string tangle with four loops outside of the tangle. We determine a biologically relevant 4-string tangle model. We also develop mathematics for solving 4-string tangle equations to determine the topology of DNA within a protein complex.

Three-Dimensional Structure of Cloned T3 Connector Protein at 1.6nm Resolution

1990 ◽  
Vol 48 (1) ◽  
pp. 282-283
Author(s):  
José L. Carrascosa ◽  
José M. Valpuesta ◽  
Hisao Fujisawa
Keyword(s):  
Dna Sequences ◽  
Expression Vector ◽  
Three Dimensional ◽  
Deae Cellulose ◽  
Dna Packaging ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Freezing And Thawing ◽  
Three Dimensional Structure ◽  
Dimensional Reconstruction

The head to tail connector of bacteriophages plays a fundamental role in the assembly of viral heads and DNA packaging. In spite of the absence of sequence homology, the structure of connectors from different viruses (T4, Ø29, T3, P22, etc) share common morphological features, that are most clearly revealed in their three-dimensional structure. We have studied the three-dimensional reconstruction of the connector protein from phage T3 (gp 8) from tilted view of two dimensional crystals obtained from this protein after cloning and purification.DNA sequences including gene 8 from phage T3 were cloned, into Bam Hl-Eco Rl sites down stream of lambda promotor PL, in the expression vector pNT45 under the control of cI857. E R204 (pNT89) cells were incubated at 42°C for 2h, harvested and resuspended in 20 mM Tris HC1 (pH 7.4), 7mM 2 mercaptoethanol, ImM EDTA. The cells were lysed by freezing and thawing in the presence of lysozyme (lmg/ml) and ligthly sonicated. The low speed supernatant was precipitated by ammonium sulfate (60% saturated) and dissolved in the original buffer to be subjected to gel nitration through Sepharose 6B, followed by phosphocellulose colum (Pll) and DEAE cellulose colum (DE52). Purified gp8 appeared at 0.3M NaCl and formed crystals when its concentration increased above 1.5 mg/ml.

scholarly journals Publisher Correction: Predicting Subtype Selectivity for Adenosine Receptor Ligands with Three-Dimensional Biologically Relevant Spectrum (BRS-3D)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Song-Bing He ◽  
Ben Hu ◽  
Zheng-Kun Kuang ◽  
Dong Wang ◽  
De-Xin Kong
Keyword(s):  
Adenosine Receptor ◽  
Three Dimensional ◽  
Receptor Ligands ◽  
Biologically Relevant ◽  
Subtype Selectivity ◽  
Adenosine Receptor Ligands

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals Application of Cryo-Electron Microscopy on Drug Discovery

2021 ◽  
Vol 27 (S1) ◽  
pp. 3250-3250
Author(s):  
Viswanath Vittaladevaram ◽  
Kranthi Kuruti
Keyword(s):  
Electron Microscopy ◽  
Protein Complexes ◽  
Lead Discovery ◽  
Biologically Relevant ◽  
Biological Targets ◽  
3 Dimensional ◽  
Drug Molecules ◽  
Cryo Electron Microscopy ◽  
Therapeutic Molecules ◽  
Novel Drug

AbstractThe key aspect for development of novel drug molecules is to perform structural determination of target molecule associated with its ligand. One such tool that provides insights towards structure of molecule is Cryo-electron microscopy which covers biological targets that are intractable. Examination of proteins can be carried out in native state, as the samples are frozen at -175 degree Celsius i.e. cryogenic temperatures. In addition to this, there were no limits for molecular and functional structures of proteins that can be imagined in 3-dimensional form. This includes ligands which unravel mechanisms that are biologically relevant. This will enable to better understand the mechanisms that are used for development of new therapeutics. Application of Cryo-electron microscopy is not limited to protein complexes and is considered as non-specific. Intervention of Cryo-EM would allow to analyse the structures and also able to dissect the interaction with therapeutic molecules. The study determines the usage of cryo-EM for providing resolutions that are acceptable for lead discovery. It also provides support for lead optimization and also for discovery of vaccines and therapeutics.

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

scholarly journals The major histocompatibility complex class II promoter-binding protein RFX (NF-X) is a methylated DNA-binding protein.

1993 ◽  
Vol 13 (11) ◽  
pp. 6810-6818 ◽  
Author(s):  
X Y Zhang ◽  
N Jabrane-Ferrat ◽  
C K Asiedu ◽  
S Samac ◽  
B M Peterlin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Dna Sequences ◽  
Protein Complexes ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Class Ii ◽  
Major Histocompatibility ◽  
Methylated Dna ◽  
Mammalian Protein

A mammalian protein called RFX or NF-X binds to the X box (or X1 box) in the promoters of a number of major histocompatibility (MHC) class II genes. In this study, RFX was shown to have the same DNA-binding specificity as methylated DNA-binding protein (MDBP), and its own cDNA was found to contain a binding site for MDBP in the leader region. MDBP is a ubiquitous mammalian protein that binds to certain DNA sequences preferentially when they are CpG methylated and to other related sequences, like the X box, irrespective of DNA methylation. MDBP from HeLa and Raji cells formed DNA-protein complexes with X-box oligonucleotides that coelectrophoresed with those containing standard MDBP sites. Furthermore, MDBP and X-box oligonucleotides cross-competed for the formation of these DNA-protein complexes. DNA-protein complexes obtained with MDBP sites displayed the same partial supershifting with an antiserum directed to the N terminus of RFX seen for complexes containing an X-box oligonucleotide. Also, the in vitro-transcribed-translated product of a recombinant RFX cDNA bound specifically to MDBP ligands and displayed the DNA methylation-dependent binding of MDBP. RFX therefore contains MDBP activity and thereby also EF-C, EP, and MIF activities that are indistinguishable from MDBP and that bind to methylation-independent sites in the transcriptional enhancers of polyomavirus and hepatitis B virus and to an intron of c-myc.

scholarly journals A three dimensional ball quotient

2013 ◽  
Vol 276 (1-2) ◽  
pp. 345-370
Author(s):  
Eberhard Freitag ◽  
Riccardo Salvati Manni
Keyword(s):  
Three Dimensional ◽  
Dimensional Ball

scholarly journals Protein Complexes Detection Based on Node Local Properties and Gene Expression On PPI Weighted Networks

2021 ◽  
Author(s):  
Yang Yu ◽  
Dezhou Kong
Keyword(s):  
Gene Expression ◽  
Resource Allocation ◽  
Protein Complex ◽  
Protein Complexes ◽  
Second Order ◽  
Topological Properties ◽  
Ppi Network ◽  
Weighted Networks ◽  
Gene Expression Information ◽  
Local Properties

Abstract Background Identifying protein complexes from protein–protein interaction (PPI) networks is a crucial task, and many related algorithms have been developed to solve this issue. These algorithms usually consider a node’s direct neighbors and ignore resource allocation and second-order neighbors. The effective use of such information is crucial to protein complex detection.Results To overcome this deficiency, this paper proposes a new protein complex identification method based on node-local topological properties and gene expression information on a new weighted PPI network, named NLPGE-WPN (joint node-local topological properties and gene expression information on weighted PPI network). First, based on the resource allocation of the PPI network and gene expression, a new weight metric is designed to describe the interaction between proteins. Second, our method constructs a series of dense complex cores based on density and network diameter constraints; the final complexes are recognized by expanding the second-order neighbor nodes of core complexes. Experimental results demonstrate that this algorithm has improved the performances of precision and f-measure, which is more valid in identifying protein complexes．Conclusions This identification method is simple and can accurately identify more complexes by integrating node-local properties and gene expression on PPI weighted networks.

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