Identification of three sequence-specific DNA-binding proteins which interact with the Rous sarcoma virus enhancer and upstream promoter elements.

1988 ◽  
Vol 62 (6) ◽  
pp. 2186-2190 ◽  
Author(s):  
G H Goodwin
Keyword(s):  
Dna Binding ◽  
Rous Sarcoma Virus ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Promoter Elements ◽  
Rous Sarcoma ◽  
Upstream Promoter ◽  
Sarcoma Virus

scholarly journals A Possible Role for the Asymmetric C-Terminal Domain Dimer of Rous Sarcoma Virus Integrase in Viral DNA Binding

PLoS ONE ◽  
2013 ◽  
Vol 8 (2) ◽  
pp. e56892 ◽  
Author(s):  
Ke Shi ◽  
Krishan K. Pandey ◽  
Sibes Bera ◽  
Ajaykumar C. Vora ◽  
Duane P. Grandgenett ◽  
...  
Keyword(s):  
Dna Binding ◽  
Rous Sarcoma Virus ◽  
Viral Dna ◽  
Terminal Domain ◽  
Rous Sarcoma ◽  
Sarcoma Virus

scholarly journals Characterization of the DNA-Binding Domain of the Avian Y-Box Protein, chkYB-2, and Mutational Analysis of Its Single-Strand Binding Motif in the Rous Sarcoma Virus Enhancer

1998 ◽  
Vol 72 (2) ◽  
pp. 900-909 ◽  
Author(s):  
Ashok Nambiar ◽  
S. K. Swamynathan ◽  
Jagannadha C. Kandala ◽  
Ramareddy V. Guntaka
Keyword(s):  
Dna Binding ◽  
Rous Sarcoma Virus ◽  
Mutational Analysis ◽  
Binding Domain ◽  
Single Strand ◽  
Dna Binding Domain ◽  
Single Stranded Dna ◽  
High Affinity ◽  
Rous Sarcoma ◽  
Sarcoma Virus

ABSTRACT chkYB-2 is a sequence-specific, single-stranded DNA binding chicken Y-box protein that promotes Rous sarcoma virus long terminal repeat (RSV LTR)-driven transcription in avian fibroblasts. The DNA-binding domain of chkYB-2 has been mapped by characterizing the DNA binding properties of purified recombinant chkYB-2 mutant polypeptides. The data indicate that the invariant cold shock domain (CSD) is necessary but not sufficient for association with DNA and suggest that another conserved region, adjacent to the carboxyl boundary of the CSD, plays a role in high-affinity DNA binding. chkYB-2 binds to a tandem repeat of the 5′-GTACCACC-3′ motif on the RSV LTR. Mutational analysis of this recognition sequence revealed the requirement of an essentially unaltered template for both high-affinity binding by chkYB-2 as well as maximal transcriptional activity of the RSV LTR in vivo. The single-stranded DNA binding activity of chkYB-2 is augmented by Mg2+. The possible significance of this finding for transactivation by a single-strand DNA binding protein is discussed.

Purification and properties of the Rous sarcoma virus internal enhancer binding factor

1989 ◽  
Vol 9 (5) ◽  
pp. 1929-1939
Author(s):  
L Karnitz ◽  
D Poon ◽  
P A Weil ◽  
R Chalkley
Keyword(s):  
Molecular Weight ◽  
Dna Binding ◽  
Rous Sarcoma Virus ◽  
Sodium Dodecyl ◽  
Bhk Cells ◽  
Rous Sarcoma ◽  
Binding Factor ◽  
Sarcoma Virus

The internal enhancer binding factor (IBF) that specifically binds sequences within the gag gene internal enhancer of Rous sarcoma virus Schmidt-Ruppin A was purified to near homogeneity from BHK cells. The polypeptides that constituted IBF DNA-binding activity were identified by sodium dodecyl sulfate-polyacrylamide gel analysis. As isolated from BHK cells, IBF consisted of two different but related polypeptides. One (IBF alpha) had a molecular weight of 40,000; the other (IBF beta) had a molecular weight of 20,000 and appeared to be a proteolytic product of IBF alpha. The site within the gag gene to which IBF bounds in vitro (internal enhancer site 2; nucleotides 856 to 878 of the Rous sarcoma virus genome) were demonstrated to function as a cis-acting transcriptional stimulatory element both in vivo and in vitro. By using HeLa cell nuclear transcription extracts, purified IBF was found to function as a trans-acting transcription factor that stimulated transcription in vitro. Purified IBF was also demonstrated to be very similar to EBP20 (K. Carlberg, T. A. Ryden, and K. Beemon, J. Virol. 62:1617-1624, 1988), and it may well belong to the same family of DNA-binding proteins.

scholarly journals Purification and properties of the Rous sarcoma virus internal enhancer binding factor.

1989 ◽  
Vol 9 (5) ◽  
pp. 1929-1939 ◽  
Author(s):  
L Karnitz ◽  
D Poon ◽  
P A Weil ◽  
R Chalkley
Keyword(s):  
Molecular Weight ◽  
Dna Binding ◽  
Rous Sarcoma Virus ◽  
Sodium Dodecyl ◽  
Bhk Cells ◽  
Rous Sarcoma ◽  
Binding Factor ◽  
Sarcoma Virus

The internal enhancer binding factor (IBF) that specifically binds sequences within the gag gene internal enhancer of Rous sarcoma virus Schmidt-Ruppin A was purified to near homogeneity from BHK cells. The polypeptides that constituted IBF DNA-binding activity were identified by sodium dodecyl sulfate-polyacrylamide gel analysis. As isolated from BHK cells, IBF consisted of two different but related polypeptides. One (IBF alpha) had a molecular weight of 40,000; the other (IBF beta) had a molecular weight of 20,000 and appeared to be a proteolytic product of IBF alpha. The site within the gag gene to which IBF bounds in vitro (internal enhancer site 2; nucleotides 856 to 878 of the Rous sarcoma virus genome) were demonstrated to function as a cis-acting transcriptional stimulatory element both in vivo and in vitro. By using HeLa cell nuclear transcription extracts, purified IBF was found to function as a trans-acting transcription factor that stimulated transcription in vitro. Purified IBF was also demonstrated to be very similar to EBP20 (K. Carlberg, T. A. Ryden, and K. Beemon, J. Virol. 62:1617-1624, 1988), and it may well belong to the same family of DNA-binding proteins.

DBP-PSSM: Combination of evolutionary profiles with the XGBoost algorithm to improve the identification of DNA-binding proteins

2020 ◽  
Vol 23 ◽  
Author(s):  
Yanping Zhang ◽  
Pengcheng Chen ◽  
Ya Gao ◽  
Jianwei Ni ◽  
Xiaosheng Wang
Keyword(s):  
Logistic Regression ◽  
Protein Structure ◽  
Dna Binding ◽  
Molecular Biology ◽  
Binding Proteins ◽  
Protein Sequences ◽  
Low Complexity ◽  
Dna Binding Proteins ◽  
Position Information ◽  
Position Representation

Aim and Objective:: Given the rapidly increasing number of molecular biology data available, computational methods of low complexity are necessary to infer protein structure, function, and evolution. Method:: In the work, we proposed a novel mthod, FermatS, which based on the global position information and local position representation from the curve and normalized moments of inertia, respectively, to extract features information of protein sequences. Furthermore, we use the generated features by FermatS method to analyze the similarity/dissimilarity of nine ND5 proteins and establish the prediction model of DNA-binding proteins based on logistic regression with 5-fold crossvalidation. Results:: In the similarity/dissimilarity analysis of nine ND5 proteins, the results are consistent with evolutionary theory. Moreover, this method can effectively predict the DNA-binding proteins in realistic situations. Conclusion:: The findings demonstrate that the proposed method is effective for comparing, recognizing and predicting protein sequences. The main code and datasets can download from https://github.com/GaoYa1122/FermatS.

Sign in / Sign up

Export Citation Format

Share Document