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Isorna I, González-Moles MÁ, Muñoz M, Esteban F. Substance P and Neurokinin-1 Receptor System in Thyroid Cancer: Potential Targets for New Molecular Therapies. J Clin Med 2023; 12:6409. [PMID: 37835053 PMCID: PMC10573850 DOI: 10.3390/jcm12196409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/11/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
In recent years, numerous approaches have been developed to comprehend the molecular alterations underlying thyroid cancer (TC) oncogenesis and explore novel therapeutic strategies for TC. It is now well established that the neurokinin-1 receptor (NK-1R) is overexpressed in cancer cells and that NK-1R is essential for the viability of cancer cells. The binding of substance P (SP) to NK-1R in neoplastic cells plays a pivotal role in cancer progression by promoting neoplastic cell growth, protecting tumor cells from apoptosis, triggering invasion and metastasis through the enhanced migration of cancer cells, and stimulating endothelial cell proliferation for tumor angiogenesis. Remarkably, all types of human TC (papillary, follicular, medullary, anaplastic), as well as metastatic lesions, exhibit the overexpression of SP and NK-1R compared to the normal thyroid gland. TC cells synthesize and release SP, which exerts its multiple functions through autocrine, paracrine, intracrine, and neuroendocrine processes, including the regulation of tumor burden. Consequently, the secretion of SP from TC results in increased SP levels in plasma, which are significantly higher in TC patients compared to controls. Additionally, NK-1R antagonists have demonstrated a dose-dependent antitumor action. They impair cancer cell proliferation on one side and induce apoptosis of tumor cells on the other side. Furthermore, it has been demonstrated that NK-1R antagonists inhibit neoplastic cell migration, thereby impairing both invasiveness and metastatic abilities, as well as angiogenesis. Given the consistent overexpression of NK-1R in all types of TC, targeting this receptor represents a promising therapeutic approach for TC. Therefore, NK-1R antagonists, such as the drug aprepitant, may represent novel drugs for TC treatment.
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Affiliation(s)
- Inmaculada Isorna
- Department of Otorhinolaryngology, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain; (I.I.); (F.E.)
| | | | - Miguel Muñoz
- Research Laboratory on Neuropeptides, Institute of Biomedicine of Seville (IBiS), 41013 Seville, Spain
| | - Francisco Esteban
- Department of Otorhinolaryngology, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain; (I.I.); (F.E.)
- School of Medicine, University of Seville, 41009 Seville, Spain
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2
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Strelnikov IA, Kovaleva NA, Klinov AP, Zubova EA. C-B-A Test of DNA Force Fields. ACS OMEGA 2023; 8:10253-10265. [PMID: 36969447 PMCID: PMC10034787 DOI: 10.1021/acsomega.2c07781] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the noncanonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B-C and B-A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar-phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.
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Das S, Roy S, Bhattacharyya D. DNA base sequence specificity through partial intercalation: DFT-D based energy analysis of molecular dynamics snapshots. J Mol Graph Model 2020; 101:107722. [DOI: 10.1016/j.jmgm.2020.107722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/27/2022]
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4
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Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature 2020; 587:291-296. [PMID: 33087930 PMCID: PMC7666076 DOI: 10.1038/s41586-020-2843-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 09/17/2020] [Indexed: 12/17/2022]
Abstract
Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription factors bind to specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood1,2. Many DNA-binding proteins induce changes in the structure of the DNA outside the intrinsic B-DNA envelope. However, how the energetic cost that is associated with distorting the DNA contributes to recognition has proven difficult to study, because the distorted DNA exists in low abundance in the unbound ensemble3-9. Here we use a high-throughput assay that we term SaMBA (saturation mismatch-binding assay) to investigate the role of DNA conformational penalties in transcription factor-DNA recognition. In SaMBA, mismatched base pairs are introduced to pre-induce structural distortions in the DNA that are much larger than those induced by changes in the Watson-Crick sequence. Notably, approximately 10% of mismatches increased transcription factor binding, and for each of the 22 transcription factors that were examined, at least one mismatch was found that increased the binding affinity. Mismatches also converted non-specific sites into high-affinity sites, and high-affinity sites into 'super sites' that exhibit stronger affinity than any known canonical binding site. Determination of high-resolution X-ray structures, combined with nuclear magnetic resonance measurements and structural analyses, showed that many of the DNA mismatches that increase binding induce distortions that are similar to those induced by protein binding-thus prepaying some of the energetic cost incurred from deforming the DNA. Our work indicates that conformational penalties are a major determinant of protein-DNA recognition, and reveals mechanisms by which mismatches can recruit transcription factors and thus modulate replication and repair activities in the cell10,11.
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Affiliation(s)
- Ariel Afek
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Harshit Sahay
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Alon Senitzki
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Mimi Fang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Raul Salinas
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Zachery Mielko
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
- Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Tali E Haran
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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5
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Morales JM, Michaelian K. Photon Dissipation as the Origin of Information Encoding in RNA and DNA. ENTROPY (BASEL, SWITZERLAND) 2020; 22:E940. [PMID: 33286709 PMCID: PMC7597208 DOI: 10.3390/e22090940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022]
Abstract
Ultraviolet light incident on organic material can initiate its spontaneous dissipative structuring into chromophores which can catalyze their own replication. This may have been the case for one of the most ancient of all chromophores dissipating the Archean UVC photon flux, the nucleic acids. Oligos of nucleic acids with affinity to particular amino acids which foment UVC photon dissipation would most efficiently catalyze their own reproduction and thus would have been selected through non-equilibrium thermodynamic imperatives which favor dissipation. Indeed, we show here that those amino acids with characteristics most relevant to fomenting UVC photon dissipation are precisely those with greatest chemical affinity to their codons or anticodons. This could provide a thermodynamic basis for the specificity in the amino acid-nucleic acid interaction and an explanation for the accumulation of information in nucleic acids since this information is relevant to the optimization of dissipation of the externally imposed thermodynamic potentials. The accumulation of information in this manner provides a link between evolution and entropy production.
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Affiliation(s)
- Julián Mejía Morales
- Postgrado in Physical Sciences, Instituto de Física, Universidad Nacional Autónoma de México, Cto. de la Investigación Científica, Cuidad Universitaria, Mexico City C.P. 04510, Mexico;
| | - Karo Michaelian
- Department of Nuclear Physics and Application of Radiation, Instituto de Física, Universidad Nacional Autónoma de México, Cto. de la Investigación Científica, Cuidad Universitaria, Mexico City C.P. 04510, Mexico
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6
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Mondal S, Bandyopadhyay S. Heterogeneous Dynamical Environment at the Interface of a Protein-DNA Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4567-4581. [PMID: 32267701 DOI: 10.1021/acs.langmuir.9b03175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Binding between protein and DNA is an essential process to regulate different biological activities. Two puzzling questions in protein-DNA recognition are (i) how the protein's binding domain identifies the DNA sequence in an aqueous solution and (ii) how the formation of the complex alters the dynamical environment around it. In this work, we present results obtained from molecular dynamics simulations of the N-terminal α-helical domain of the λ-repressor protein (in dimeric form) bound to the corresponding operator DNA. Effects of formation of the complex in modifying the microscopic dynamics of water as well as the kinetics of hydrogen bonds at the interface have been explored. Locally heterogeneous restricted water motions at the complex interface have been observed, the extent of restriction being more significant around the directly bound residues of the protein and the DNA. In particular, the calculation revealed the existence of significantly constrained motionally restricted water layer that can form either bridges around the directly bound residues of the protein and DNA or are engaged in forming water-mediated contacts between a fraction of the unbound residues. More importantly, it is observed that the restricted water motion around the complex is correlated with the hydrogen bond relaxation time scale at the interface. It is further demonstrated that the kinetics of water-water hydrogen bonds involving the bridged water are influenced more due to complex formation.
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Affiliation(s)
- Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
- Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India
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7
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Maganti L, Bhattacharyya D. Sequence specificity in DNA–drug intercalation: MD simulation and density functional theory approaches. J Comput Aided Mol Des 2019; 34:83-95. [DOI: 10.1007/s10822-019-00268-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/29/2019] [Indexed: 12/14/2022]
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8
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Mondal S, Bandyopadhyay S. Flexibility of the Binding Regions of a Protein-DNA Complex and the Structure and Ordering of Interfacial Water. J Chem Inf Model 2019; 59:4427-4437. [PMID: 31580657 DOI: 10.1021/acs.jcim.9b00685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Noncovalent interactions between protein and DNA are important to comprehend different biological activities in living organisms. One important issue is how the protein identifies the target DNA and the influence of the resulting protein-DNA complex on the hydration environment around it. In this study, we have carried out atomistic molecular dynamics simulations of the protein-DNA complex formed by the dimeric form of the α-helical N-terminal domain of the λ-repressor protein with its operator DNA. Local heterogeneous flexibilities of the residues of the protein and the DNA components that are involved in binding and the microscopic structure and ordering of water around those have been investigated in detail. The calculations revealed concurrent existence of highly ordered as well as disordered water molecules at the interface. It is found that a fraction of doubly coordinated water molecules exhibit high degree of ordering at the interface, while the randomly oriented ones are coordinated with three water molecules. The effect has been found to be more around the protein and DNA residues that are in contact in the complexed state. We believe that such highly ordered two-coordinated water molecules are likely to act as an adhesive to facilitate the formation of a protein-DNA complex and maintain its structural stability.
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9
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Zheng L, Shi J, Mu Y. Dynamics changes of CRISPR-Cas9 systems induced by high fidelity mutations. Phys Chem Chem Phys 2018; 20:27439-27448. [DOI: 10.1039/c8cp04226h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas9, a powerful genome editing tool, has widely been applied in biological fields.
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Affiliation(s)
- Liangzhen Zheng
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Jiahai Shi
- Department of Biomedical Sciences
- College of Veterinary Medicine and Life Sciences
- City University of Hong Kong
- Hong Kong SAR
- City University of Hong Kong Shenzhen Research Institute
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
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10
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Mazumder A, Batabyal S, Mondal M, Mondol T, Choudhury S, Ghosh R, Chatterjee T, Bhattacharyya D, Pal SK, Roy S. Specific DNA sequences allosterically enhance protein-protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation. Phys Chem Chem Phys 2017; 19:14781-14792. [PMID: 28548177 DOI: 10.1039/c7cp01193h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Most genes are regulated by multiple transcription factors, often assembling into multi-protein complexes in the gene regulatory region. Understanding of the molecular origin of specificity of gene regulatory complex formation in the context of the whole genome is currently inadequate. A phage transcription factor λ-CI forms repressive multi-protein complexes by binding to multiple binding sites in the genome to regulate the lifecycle of the phage. The protein-protein interaction between two DNA-bound λ-CI molecules is stronger when they are bound to the correct pair of binding sites, suggesting allosteric transmission of recognition of correct DNA sequences to the protein-protein interaction interface. Exploration of conformation and dynamics by time-resolved fluorescence anisotropy decay and molecular dynamics suggests a change in protein dynamics to be a crucial factor in mediating allostery. A lattice-based model suggests that DNA-sequence induced allosteric effects could be crucial underlying factors in differentially stabilizing the correct site-specific gene regulatory complexes. We conclude that transcription factors have evolved multiple mechanisms to augment the specificity of DNA-protein interactions in order to achieve an extraordinarily high degree of spatial and temporal specificities of gene regulatory complexes, and DNA-sequence induced allostery plays an important role in the formation of sequence-specific gene regulatory complexes.
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Affiliation(s)
- Abhishek Mazumder
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700 032, India
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11
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Mondal S, Chakraborty K, Bandyopadhyay S. Microscopic understanding of the conformational features of a protein–DNA complex. Phys Chem Chem Phys 2017; 19:32459-32472. [DOI: 10.1039/c7cp05161a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein–DNA interactions play crucial roles in different stages of genetic activities, such as replication of genome, initiation of transcription,etc.
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Affiliation(s)
- Sandip Mondal
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Kaushik Chakraborty
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
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12
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Ramachandrakurup S, Ammapalli S, Ramakrishnan V. Investigating the effect of charged amino acids on DNA conformation in EcoRI-DNA complex: a molecular dynamics simulation study. J Biomol Struct Dyn 2016; 35:3540-3554. [PMID: 27935429 DOI: 10.1080/07391102.2016.1261741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Sequence-specific binding of proteins to DNA is essential for almost all the cellular processes like transcription, translation, replication, etc. One among the various mechanisms that has been identified so far that contributes to the specificity in protein-DNA interaction is the DNA conformational change. Electrostatic neutralization of the phosphate groups by the positively charged amino acid residues in proteins is thought to bring about such conformational changes in DNA. Here, we employ molecular dynamics simulations to examine the effect of charge on amino acids Lys113, Arg145, and Asp91 which are attached to the scissile phosphate on the conformation of DNA in EcoRI-DNA complex. The results indicate that the charge of these amino acids is essential for maintaining the local conformation of DNA in the EcoRI-bound form. Interestingly, we observe that the positively charged amino acids Lys113 and Arg145 have a long-range influence on the DNA conformation, whereas the negatively charged amino acid Asp91 has only a localized effect on the DNA conformation. The charge on the amino acids also alters the collective dynamics of EcoRI. Collectively, the results shed light on the diversity of the effect of charges on DNA conformation as well as on protein dynamics.
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Affiliation(s)
| | - Sumanth Ammapalli
- a School of Chemical and Biotechnology , SASTRA University , Thanjavur 613401 , India
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Arkova O, Kuznetsov N, Fedorova O, Savinkova L. A real-time study of the interaction of TBP with a TATA box-containing duplex identical to an ancestral or minor allele of human gene LEP or TPI. J Biomol Struct Dyn 2016; 35:3070-3081. [PMID: 27667393 DOI: 10.1080/07391102.2016.1241190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
It is known that only a single-nucleotide substitution (SNP: a single nucleotide polymorphism) in the sequence of a TATA box can influence the affinity of the interaction of TBP with the TATA box and contribute to the pathogenesis of complex hereditary human diseases and sometimes may be a cause of monogenic diseases (for instance, β-thalassemia). In the present work, we studied the interaction of human TBP with a double-stranded oligodeoxyribonucleotide (ODN) 15 or 26 bp long identical to a TATA box of promoters of a real-life human gene, TPI or LEP, and labeled with fluorophores TAMRA and FAM. To analyze the interaction of TBP with a TATA box of an ancestral or minor allele (SNP in the TATA box) in real time, we used the stopped-flow method with detection of a Förster resonance energy transfer (FRET) signal. The nature of the resulting kinetic curves reflecting changes in the FRET signal (and therefore of DNA conformation during the interaction with TBP) pointed to a multistage mechanism of the formation of the TBP complex with the TATA-containing ODN. The results showed that with the increasing concentration and length of the ODN, heterogeneity of conformational changes (taking place during the first second of the interaction with TBP) in DNA also increases. In contrast to the initial nonspecific interaction, the subsequent phases strictly depend on TBP concentration: at the TBP:ODN ratio of 10:1, the velocity of change of the FRET signal increases approximately 100-fold.
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Affiliation(s)
- Olga Arkova
- a Institute of Cytology and Genetics (ICG) , Siberian Branch of Russian Academy of Sciences (SB RAS) , Lavrentyev Ave. 10, Novosibirsk 630090 , Russia
| | - Nikita Kuznetsov
- b Institute of Chemical Biology and Fundamental Medicine (ICBFM) , Siberian Branch of Russian Academy of Sciences (SB RAS) , Lavrentyev Ave. 8, Novosibirsk 630090 , Russia
| | - Olga Fedorova
- b Institute of Chemical Biology and Fundamental Medicine (ICBFM) , Siberian Branch of Russian Academy of Sciences (SB RAS) , Lavrentyev Ave. 8, Novosibirsk 630090 , Russia
| | - Ludmila Savinkova
- a Institute of Cytology and Genetics (ICG) , Siberian Branch of Russian Academy of Sciences (SB RAS) , Lavrentyev Ave. 10, Novosibirsk 630090 , Russia
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14
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Role of indirect readout mechanism in TATA box binding protein-DNA interaction. J Comput Aided Mol Des 2015; 29:283-95. [PMID: 25575717 DOI: 10.1007/s10822-014-9828-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/18/2014] [Indexed: 12/11/2022]
Abstract
Gene expression generally initiates from recognition of TATA-box binding protein (TBP) to the minor groove of DNA of TATA box sequence where the DNA structure is significantly different from B-DNA. We have carried out molecular dynamics simulation studies of TBP-DNA system to understand how the DNA structure alters for efficient binding. We observed rigid nature of the protein while the DNA of TATA box sequence has an inherent flexibility in terms of bending and minor groove widening. The bending analysis of the free DNA and the TBP bound DNA systems indicate presence of some similar structures. Principal coordinate ordination analysis also indicates some structural features of the protein bound and free DNA are similar. Thus we suggest that the DNA of TATA box sequence regularly oscillates between several alternate structures and the one suitable for TBP binding is induced further by the protein for proper complex formation.
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