Dynamical perspective of protein-DNA interaction

2014 ◽  
Vol 5 (1) ◽  
pp. 21-43 ◽  
Author(s):  
Subrata Batabyal ◽  
Susobhan Choudhury ◽  
Dilip Sao ◽  
Tanumoy Mondol ◽  
Samir Kumar Pal
Keyword(s):  
Biological Activities ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Dna Interaction ◽  
Specific Protein ◽  
Water Dynamics ◽  
Dna Interactions ◽  
Terminal Domain ◽  
Protein Dna Interactions ◽  
Dna Complex

AbstractThe interactions between protein-DNA are essential for various biological activities. In this review, we provide an overview of protein-DNA interactions that emphasizes the importance of dynamical aspects. We divide protein-DNA interactions into two categories: nonspecific and specific and both the categories would be discussed highlighting some of our relevant work. In the case of nonspecific protein-DNA interaction, solvation studies (picosecond and femtosecond-resolved) explore the role environmental dynamics and change in the micropolarity around DNA molecules upon complexation with histone protein (H1). While exploring the specific protein-DNA interaction at λ-repressor-operator sites interaction, particularly OR1 and OR2, it was observed that the interfacial water dynamics is minimally perturbed upon interaction with DNA, suggesting the labile interface in the protein-DNA complex. Förster resonance energy transfer (FRET) study revealed that the structure of the protein is more compact in repressor-OR2 complex than in the repressor-OR1 complex. Fluorescence anisotropy studies indicated enhanced flexibility of the C-terminal domain of the repressor at fast timescales after complex formation with OR1. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with OR1 DNA compared to OR2 DNA were found to have pronounced effect on the rate of photoinduced electron transfer.

Halophilic adaptation of protein–DNA interactions

2003 ◽  
Vol 31 (3) ◽  
pp. 677-680 ◽  
Author(s):  
S. Bergqvist ◽  
M.A. Williams ◽  
R. O'Brien ◽  
J.E. Ladbury
Keyword(s):  
Dna Interaction ◽  
Dna Interactions ◽  
Evolutionary Time ◽  
Homologous Proteins ◽  
Binding Characteristics ◽  
Dna Binding Site ◽  
Protein Dna Interactions ◽  
Tata Box Binding Protein ◽  
Dna Complex ◽  
Halophilic Adaptation

Pyrococcus woesei (Pw) is an archaeal organism adapted to living in conditions of elevated salt and temperature. Thermodynamic data reveal that the interaction between the TATA-box-binding protein (TBP) from this organism and DNA has an entirely different character to the same interaction in mesophilic counterparts. In the case of the PwTBP, the affinity of its interaction with DNA increases with increasing salt concentration. The opposite effect is observed in all known mesophilic protein–DNA interactions. The halophilic behaviour can be attributed to sequestration of cations into the protein–DNA complex. By mutating residues in the PwTBP DNA-binding site, potential sites of cation interaction can be removed. These mutations have a significant effect on the binding characteristics, and the halophilic nature of the PwTBP–DNA interaction can be reversed, and made to resemble that of a mesophile, in just three mutations. The genes of functionally homologous proteins in organisms existing in different environments show that adaptation is most often accompanied by mutation of an existing protein. However, the importance of any individual residue to a phenotypic characteristic is usually difficult to assess amongst the multitude of changes that occur over evolutionary time. Since the halophilic nature of this protein can be attributed to only three mutations, this reveals that the important phenotype of halophilicity could be rapidly acquired in evolutionary time.

Microscopic understanding of the conformational features of a protein–DNA complex

2017 ◽  
Vol 19 (48) ◽  
pp. 32459-32472 ◽  
Author(s):  
Sandip Mondal ◽  
Kaushik Chakraborty ◽  
Sanjoy Bandyopadhyay
Keyword(s):  
Dna Interactions ◽  
P Protein ◽  
Protein Dna Interactions ◽  
Initiation Of Transcription ◽  
Dna Complex

Protein–DNA interactions play crucial roles in different stages of genetic activities, such as replication of genome, initiation of transcription,etc.

scholarly journals Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Alexandra Stützer ◽  
Luisa M. Welp ◽  
Monika Raabe ◽  
Timo Sachsenberg ◽  
Christin Kappert ◽  
...  
Keyword(s):  
Uv Light ◽  
Amino Acid Level ◽  
Dna Interaction ◽  
Cross Linking ◽  
Dna Interactions ◽  
Single Experiment ◽  
Protein Dna Interactions ◽  
Nucleosome Binding ◽  
Binding Interfaces

Abstract Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by ultraviolet (UV) light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain insights into chromatin and its regulation in the future.

scholarly journals Facilitation of DNA loop formation by protein–DNA non-specific interactions

Soft Matter ◽  
2019 ◽  
Vol 15 (26) ◽  
pp. 5255-5263 ◽  
Author(s):  
Jaeoh Shin ◽  
Anatoly B. Kolomeisky
Keyword(s):  
Specific Protein ◽  
Dna Looping ◽  
Specific Interactions ◽  
Loop Formation ◽  
Dna Interactions ◽  
Dna Loop ◽  
Protein Dna Interactions

DNA looping is facilitated by non-specific protein–DNA interactions.

scholarly journals Dynamic structural insights into the molecular mechanism of DNA unwinding by the bacteriophage T7 helicase

2020 ◽  
Vol 48 (6) ◽  
pp. 3156-3164 ◽  
Author(s):  
Jian-Bing Ma ◽  
Ze Chen ◽  
Chun-Hua Xu ◽  
Xing-Yuan Huang ◽  
Qi Jia ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Molecular Mechanism ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Bacteriophage T7 ◽  
Dna Unwinding ◽  
Coupling Mechanism ◽  
Mechanical Coupling ◽  
Dna Complex ◽  
Structural Insights

Abstract The hexametric T7 helicase (gp4) adopts a spiral lock-washer form and encircles a coil-like DNA (tracking) strand with two nucleotides bound to each subunit. However, the chemo-mechanical coupling mechanism in unwinding has yet to be elucidated. Here, we utilized nanotensioner-enhanced Förster resonance energy transfer with one nucleotide precision to investigate gp4-induced unwinding of DNA that contains an abasic lesion. We observed that the DNA unwinding activity of gp4 is hindered but not completely blocked by abasic lesions. Gp4 moves back and forth repeatedly when it encounters an abasic lesion, whereas it steps back only occasionally when it unwinds normal DNA. We further observed that gp4 translocates on the tracking strand in step sizes of one to four nucleotides. We propose that a hypothetical intermediate conformation of the gp4–DNA complex during DNA unwinding can help explain how gp4 molecules pass lesions, providing insights into the unwinding dynamics of gp4.

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