Interactions at the nucleic acid binding site of the avian retroviral nucleocapsid protein: studies utilizing the fluorescent probe 4,4'-bis(phenylamino)(1,1'-binaphthalene)-5,5'-disulfonic acid

HIV-1 Gag polyprotein orchestrates the assembly of viral particles. Its C-terminus consists of the nucleocapsid (NC) domain that interacts with nucleic acids, and p1 and p6, two unstructured regions, p6 containing the motifs to bind ALIX, the cellular ESCRT factor TSG101 and the viral protein Vpr. The processing of Gag by the viral protease subsequently liberates NCp15 (NC-p1-p6), NCp9 (NC-p1) and NCp7, NCp7 displaying the optimal chaperone activity of nucleic acids. This review focuses on the nucleic acid binding properties of the NC domain in the different maturation states during the HIV-1 viral cycle.

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Details of the nucleic acid binding site of T4 gene 32 protein revealed by proteolysis and DNA T m depression methods 1 1Edited by R. Ebright

Journal of Molecular Biology ◽

10.1006/jmbi.1999.2541 ◽

1999 ◽

Vol 286 (4) ◽

pp. 1107-1121 ◽

Cited By ~ 12

Author(s):

Min Wu ◽

Elizabeth K Flynn ◽

Richard L Karpel

Keyword(s):

Nucleic Acid ◽

Binding Site ◽

Nucleic Acid Binding ◽

Gene 32 ◽

T4 Gene 32 Protein

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Variability in the nucleic acid binding site size and the amount of single-stranded DNA-binding protein inEscherichia coli

FEBS Letters ◽

10.1016/0014-5793(85)81128-5 ◽

1985 ◽

Vol 181 (1) ◽

pp. 133-137 ◽

Cited By ~ 21

Author(s):

E.V. Bobst ◽

A.M. Bobst ◽

F.W. Perrino ◽

R.R. Meyer ◽

D.C. Rein

Keyword(s):

Nucleic Acid ◽

Dna Binding ◽

Binding Site ◽

Binding Protein ◽

Dna Binding Protein ◽

Inescherichia Coli ◽

Nucleic Acid Binding ◽

Single Stranded Dna

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Fluorescence and nucleic acid binding properties of the human T-cell leukemia virus-type 1 nucleocapsid protein

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology ◽

10.1016/s0167-4838(00)00181-3 ◽

2000 ◽

Vol 1481 (2) ◽

pp. 381-394 ◽

Cited By ~ 13

Author(s):

David R Morcock ◽

Bradley P Kane ◽

José R Casas-Finet

Keyword(s):

Nucleic Acid ◽

Nucleocapsid Protein ◽

Leukemia Virus ◽

Nucleic Acid Binding ◽

Cell Leukemia ◽

Binding Properties ◽

Cell Leukemia Virus Type ◽

Human T Cell ◽

T Cell Leukemia Virus

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Nuclear Magnetic Resonance Structure of the Nucleic Acid-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein 3

Journal of Virology ◽

10.1128/jvi.01253-09 ◽

2009 ◽

Vol 83 (24) ◽

pp. 12998-13008 ◽

Cited By ~ 38

Author(s):

Pedro Serrano ◽

Margaret A. Johnson ◽

Amarnath Chatterjee ◽

Benjamin W. Neuman ◽

Jeremiah S. Joseph ◽

...

Keyword(s):

Nuclear Magnetic Resonance ◽

Nucleic Acid ◽

Magnetic Resonance ◽

Severe Acute Respiratory Syndrome ◽

Binding Site ◽

Nonstructural Protein ◽

Globular Domain ◽

Nucleic Acid Binding ◽

Nonstructural Protein 3 ◽

Nuclear Magnetic

ABSTRACT The nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand β-sheet holding two α-helices of three and four turns that are oriented antiparallel to the β-strands. Two antiparallel two-strand β-sheets and two 310-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold.

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An Overview of Computational Tools of Nucleic Acid Binding Site Prediction for Site-specific Proteins and Nucleases

Protein and Peptide Letters ◽

10.2174/0929866526666191028162302 ◽

2020 ◽

Vol 27 (5) ◽

pp. 370-384

Author(s):

Hua Wan ◽

Jian-ming Li ◽

Huang Ding ◽

Shuo-xin Lin ◽

Shu-qin Tu ◽

...

Keyword(s):

Nucleic Acid ◽

Binding Site ◽

Genome Editing ◽

Computational Methods ◽

Target Prediction ◽

Support Vector ◽

Nucleic Acid Binding ◽

Computational Tools ◽

Site Specific ◽

Specific Proteins

: Understanding the interaction mechanism of proteins and nucleic acids is one of the most fundamental problems for genome editing with engineered nucleases. Due to some limitations of experimental investigations, computational methods have played an important role in obtaining the knowledge of protein-nucleic acid interaction. Over the past few years, dozens of computational tools have been used for identification of nucleic acid binding site for site-specific proteins and design of site-specific nucleases because of their significant advantages in genome editing. Here, we review existing widely-used computational tools for target prediction of site-specific proteins as well as off-target prediction of site-specific nucleases. This article provides a list of on-line prediction tools according to their features followed by the description of computational methods used by these tools, which range from various sequence mapping algorithms (like Bowtie, FetchGWI and BLAST) to different machine learning methods (such as Support Vector Machine, hidden Markov models, Random Forest, elastic network and deep neural networks). We also make suggestions on the further development in improving the accuracy of prediction methods. This survey will provide a reference guide for computational biologists working in the field of genome editing.

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