Human nuclear receptors (NRs) are a superfamily of ligand-responsive transcription factors that h... more Human nuclear receptors (NRs) are a superfamily of ligand-responsive transcription factors that have central roles in cellular function. Their malfunction is linked to numerous diseases, and the ability to modulate their activity with synthetic ligands has yielded 16% of all FDA-approved drugs. NRs regulate distinct gene networks, however they often function from genomic sites that lack known binding motifs. Here, to annotate genomic binding sites of known and unexamined NRs more accurately, we use high-throughput SELEX to comprehensively map DNA binding site preferences of all full-length human NRs, in complex with their ligands. Furthermore, to identify non-obvious binding sites buried in DNA–protein interactomes, we develop MinSeq Find, a search algorithm based on the MinTerm concept from electrical engineering and digital systems design. The resulting MinTerm sequence set (MinSeqs) reveal a constellation of binding sites that more effectively annotate NR-binding profiles in cell...
... 242 Aditi Kanhere and Manju Bansal are nearly perpendicular to the helix axis, there is a mar... more ... 242 Aditi Kanhere and Manju Bansal are nearly perpendicular to the helix axis, there is a marked change in the direction of the helix axis at ... structures (Reproduced from Bansal 1996) Data points Roll* Tilt* Twist* CA/TG(BI)* 7 5.1 -0.31 31.03 GG/CC 10 5.02 -1.83 32.4 AG/CT 6 ...
This year marks the 50th anniversary of the coiled-coil triple helical structure of collagen, fir... more This year marks the 50th anniversary of the coiled-coil triple helical structure of collagen, first proposed by Ramachandran's group from Madras. The structure is unique among the protein secondary structures in that it requires a very specific tripeptide sequence repeat, with glycine being mandatory at every third position and readily accommodates the imino acids proline/ hydroxyproline, at the other two positions. The original structure was postulated to be stabilized by two interchain hydrogen bonds, per tripeptide. Subsequent modeling studies suggested that the triple helix is stabilized by one direct inter chain hydrogen bond as well as water mediated hydrogen bonds. The hydroxyproline residues were also implicated to play an important role in stabilizing the collagen fibres. Several high resolution crystal structures of oligopeptides related to collagen have been determined in the last ten years. Stability of synthetic mimics of collagen has also been extensively studied. These have confirmed the essential correctness of the coiledcoil triple helical structure of collagen, as well as the role of water and hydroxyproline residues, but also indicated additional sequencedependent features. This review discusses some of these recent results and their implications for collagen fiber formation.
Inovirus is a helical array of α-helical protein asymmetric units surrounding a DNA core. X-ray f... more Inovirus is a helical array of α-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.
Group VII of the "Landolt-Bornstein" series is devoted to the physical properties of bi... more Group VII of the "Landolt-Bornstein" series is devoted to the physical properties of biological systems. It begins with this volume, covering nucleic acids which are of central importance in all processes involving gene expression. This field has become increasingly important during the last decade due to the development of genetic engineering. Because of the amount of data available, this text has had to be divided into several sub-volumes. The first two subvolumes, deal with crystallographic and structural data which provide information on the three dimensional structure of the nucleic acids, their folding properties, their hydrogen bonding schemes, their metal binding capabilities, their hydration and their drug complexation. This text covers the first part of spectroscopic, kinetic and physical data and the present sub-volume concludes this chapter and also deals with theoretical investigations.
Inovirus is a helical array of α-helical protein asymmetric units surrounding a DNA core. X-ray f... more Inovirus is a helical array of α-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.
Model building and molecular mechanics studies have been carried out to examine the potential str... more Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC) 5 and d(CAG/CTG) 5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures.
Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcin... more Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg128 into the DNA double helix and its interaction with the O6MG:C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.
Journal of Biomolecular Structure & Dynamics, Oct 1, 1997
Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction ... more Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a triplex comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such triplex structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.
Synthetic regular polytripeptides of the type (Gly-RZ-R3) where Rz, RB, or both, are imino acids ... more Synthetic regular polytripeptides of the type (Gly-RZ-R3) where Rz, RB, or both, are imino acids have been widely studied as model compounds for collagen. One such polytripeptide is poly(G1y-Pro-Hyp), since triplets with this sequence constitute about 10% of collagen. Recently, a new model has been proposed for this polytripeptide in which one of the three peptide bonds in the tripeptide unit is in the cis conformation, and the y-hydroxyl group of hydroxyproline forms a direct interchain hydrogen bond within the triple helix. We have confirmed this structure by model building using computer techniques, and the helical parameters obtained by us are close to the experimentally observed values. The model is also found to be comparable in stability with other models from energy considerations.
Journal of Biomolecular Structure & Dynamics, Apr 1, 1995
Molecular dynamics simulation studies on polyene antifungal antibiotic amphotericin B, its head-t... more Molecular dynamics simulation studies on polyene antifungal antibiotic amphotericin B, its head-to-tail dimeric structure and lipid - amphotericin B complex demonstrate interesting features of the flexibilities within the molecule and define the optimal interactions for the formation of a stable dimeric structure and complex with phospholipid.
Proceedings of the Indian Academy of Sciences. Section A, Physical Sciences, Oct 1, 1975
The molecular structure of collagen is now accepted to be based on a triple-stranded coiled-coil,... more The molecular structure of collagen is now accepted to be based on a triple-stranded coiled-coil, in which the three strands are held together predominantly by hydrogen bonds. Recent experimental evidence has shown that the presence of hydroxyproline residues in the third position of the repeating tripeptide unit lends additional stability to the collagen structure. In this paper, we reporta model structure, which is supported by these observations. In a model structure proposed earlier, thcre ate two hydrogen bonds per tripeptide unit, one of which is a direct interchain hydrogcn bond, whilo the second hydrogen boud can be formed via a water molecule, It has now been shown that the same water molecule can also forro a hydrogen bond with the oxygen of the ~-hydroxyl group of hydroxyproline in the third position in the sequence (GIy-R~-Rz). This hydroxyl group can also take part in an inter-triple-helix hydrogen bond. Our studies thus show the role played by hydroxyproline residues in the structure and stability of collagen.
Guanine tetrads are formed spontaneously by guanine rich sequences in the presence of certain cat... more Guanine tetrads are formed spontaneously by guanine rich sequences in the presence of certain cations. Various quadruplex helical structures, stabilized by such tetrads, apparently play an important biological role in vivo. To understand the importance of the cations, a 6 ns molecular dynamics simulation has been performed on a 7-mer G-quadruplex, surrounded by Na + counterions and explicit water molecules, but without any ions in the initial structure. Interestingly, the quadruplex structure does not fall apart, but undergoes small structural changes, which enable the solvent molecules, including Na + ions, to enter the empty central channel of structure. This channel is fully hydrated within the first 100 ps and two ions move into the central channel between 0.5 and 2 ns of MD simulation, by replacing some of the water molecules. The ions once trapped within the quadruplex channel are not expelled even during 1.5 ns of MD at 400 K. In fact they penetrate deeper into the channel to facilitate entry of additional ions, though all coordination sites within the quadruplex are not occupied even after 6.1 ns of MD simulation. The entry of cations into the central channel leads to a quadruplex structure with more favorable free energy of hydration, which is comparable to that of a fully coordinated quadruplex.
Human nuclear receptors (NRs) are a superfamily of ligand-responsive transcription factors that h... more Human nuclear receptors (NRs) are a superfamily of ligand-responsive transcription factors that have central roles in cellular function. Their malfunction is linked to numerous diseases, and the ability to modulate their activity with synthetic ligands has yielded 16% of all FDA-approved drugs. NRs regulate distinct gene networks, however they often function from genomic sites that lack known binding motifs. Here, to annotate genomic binding sites of known and unexamined NRs more accurately, we use high-throughput SELEX to comprehensively map DNA binding site preferences of all full-length human NRs, in complex with their ligands. Furthermore, to identify non-obvious binding sites buried in DNA–protein interactomes, we develop MinSeq Find, a search algorithm based on the MinTerm concept from electrical engineering and digital systems design. The resulting MinTerm sequence set (MinSeqs) reveal a constellation of binding sites that more effectively annotate NR-binding profiles in cell...
... 242 Aditi Kanhere and Manju Bansal are nearly perpendicular to the helix axis, there is a mar... more ... 242 Aditi Kanhere and Manju Bansal are nearly perpendicular to the helix axis, there is a marked change in the direction of the helix axis at ... structures (Reproduced from Bansal 1996) Data points Roll* Tilt* Twist* CA/TG(BI)* 7 5.1 -0.31 31.03 GG/CC 10 5.02 -1.83 32.4 AG/CT 6 ...
This year marks the 50th anniversary of the coiled-coil triple helical structure of collagen, fir... more This year marks the 50th anniversary of the coiled-coil triple helical structure of collagen, first proposed by Ramachandran's group from Madras. The structure is unique among the protein secondary structures in that it requires a very specific tripeptide sequence repeat, with glycine being mandatory at every third position and readily accommodates the imino acids proline/ hydroxyproline, at the other two positions. The original structure was postulated to be stabilized by two interchain hydrogen bonds, per tripeptide. Subsequent modeling studies suggested that the triple helix is stabilized by one direct inter chain hydrogen bond as well as water mediated hydrogen bonds. The hydroxyproline residues were also implicated to play an important role in stabilizing the collagen fibres. Several high resolution crystal structures of oligopeptides related to collagen have been determined in the last ten years. Stability of synthetic mimics of collagen has also been extensively studied. These have confirmed the essential correctness of the coiledcoil triple helical structure of collagen, as well as the role of water and hydroxyproline residues, but also indicated additional sequencedependent features. This review discusses some of these recent results and their implications for collagen fiber formation.
Inovirus is a helical array of α-helical protein asymmetric units surrounding a DNA core. X-ray f... more Inovirus is a helical array of α-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.
Group VII of the "Landolt-Bornstein" series is devoted to the physical properties of bi... more Group VII of the "Landolt-Bornstein" series is devoted to the physical properties of biological systems. It begins with this volume, covering nucleic acids which are of central importance in all processes involving gene expression. This field has become increasingly important during the last decade due to the development of genetic engineering. Because of the amount of data available, this text has had to be divided into several sub-volumes. The first two subvolumes, deal with crystallographic and structural data which provide information on the three dimensional structure of the nucleic acids, their folding properties, their hydrogen bonding schemes, their metal binding capabilities, their hydration and their drug complexation. This text covers the first part of spectroscopic, kinetic and physical data and the present sub-volume concludes this chapter and also deals with theoretical investigations.
Inovirus is a helical array of α-helical protein asymmetric units surrounding a DNA core. X-ray f... more Inovirus is a helical array of α-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.
Model building and molecular mechanics studies have been carried out to examine the potential str... more Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC) 5 and d(CAG/CTG) 5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures.
Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcin... more Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg128 into the DNA double helix and its interaction with the O6MG:C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.
Journal of Biomolecular Structure & Dynamics, Oct 1, 1997
Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction ... more Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a triplex comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such triplex structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.
Synthetic regular polytripeptides of the type (Gly-RZ-R3) where Rz, RB, or both, are imino acids ... more Synthetic regular polytripeptides of the type (Gly-RZ-R3) where Rz, RB, or both, are imino acids have been widely studied as model compounds for collagen. One such polytripeptide is poly(G1y-Pro-Hyp), since triplets with this sequence constitute about 10% of collagen. Recently, a new model has been proposed for this polytripeptide in which one of the three peptide bonds in the tripeptide unit is in the cis conformation, and the y-hydroxyl group of hydroxyproline forms a direct interchain hydrogen bond within the triple helix. We have confirmed this structure by model building using computer techniques, and the helical parameters obtained by us are close to the experimentally observed values. The model is also found to be comparable in stability with other models from energy considerations.
Journal of Biomolecular Structure & Dynamics, Apr 1, 1995
Molecular dynamics simulation studies on polyene antifungal antibiotic amphotericin B, its head-t... more Molecular dynamics simulation studies on polyene antifungal antibiotic amphotericin B, its head-to-tail dimeric structure and lipid - amphotericin B complex demonstrate interesting features of the flexibilities within the molecule and define the optimal interactions for the formation of a stable dimeric structure and complex with phospholipid.
Proceedings of the Indian Academy of Sciences. Section A, Physical Sciences, Oct 1, 1975
The molecular structure of collagen is now accepted to be based on a triple-stranded coiled-coil,... more The molecular structure of collagen is now accepted to be based on a triple-stranded coiled-coil, in which the three strands are held together predominantly by hydrogen bonds. Recent experimental evidence has shown that the presence of hydroxyproline residues in the third position of the repeating tripeptide unit lends additional stability to the collagen structure. In this paper, we reporta model structure, which is supported by these observations. In a model structure proposed earlier, thcre ate two hydrogen bonds per tripeptide unit, one of which is a direct interchain hydrogcn bond, whilo the second hydrogen boud can be formed via a water molecule, It has now been shown that the same water molecule can also forro a hydrogen bond with the oxygen of the ~-hydroxyl group of hydroxyproline in the third position in the sequence (GIy-R~-Rz). This hydroxyl group can also take part in an inter-triple-helix hydrogen bond. Our studies thus show the role played by hydroxyproline residues in the structure and stability of collagen.
Guanine tetrads are formed spontaneously by guanine rich sequences in the presence of certain cat... more Guanine tetrads are formed spontaneously by guanine rich sequences in the presence of certain cations. Various quadruplex helical structures, stabilized by such tetrads, apparently play an important biological role in vivo. To understand the importance of the cations, a 6 ns molecular dynamics simulation has been performed on a 7-mer G-quadruplex, surrounded by Na + counterions and explicit water molecules, but without any ions in the initial structure. Interestingly, the quadruplex structure does not fall apart, but undergoes small structural changes, which enable the solvent molecules, including Na + ions, to enter the empty central channel of structure. This channel is fully hydrated within the first 100 ps and two ions move into the central channel between 0.5 and 2 ns of MD simulation, by replacing some of the water molecules. The ions once trapped within the quadruplex channel are not expelled even during 1.5 ns of MD at 400 K. In fact they penetrate deeper into the channel to facilitate entry of additional ions, though all coordination sites within the quadruplex are not occupied even after 6.1 ns of MD simulation. The entry of cations into the central channel leads to a quadruplex structure with more favorable free energy of hydration, which is comparable to that of a fully coordinated quadruplex.
Transcription initiation is the first step in the regulation of gene expression. Promoters are th... more Transcription initiation is the first step in the regulation of gene expression. Promoters are the regions of genomic DNA where transcription initiation machinery assembles and are generally characterized by presence of short nucleotide sequence motifs like TATA-box, Inr element, BRE, etc. However, apart from these motifs, promoter regions have been reported to have structural properties, such as lower stability, lesser bendability and more curvature compared to other genomic regions. Interestingly, these properties are conserved from archaea to mammals, with little differences. Several algorithms have been developed to differentiate promoter regions from non promoters, using DNA structural properties. Here we show that, in E. coli and S. cerevisiae, genes with different experimentally determined expression levels, differ in their structural features. Promoters of highly expressed or less responsive genes are less stable, less bendable and more curved compared to promoters of lowly expressed or more responsive genes. This suggests that these structural properties can be used to design promoters to modulate gene expression. Keywords Promoter engineering · DNA structural properties · DNA duplex stability · DNA bendability · Intrinsic curvature · NUCRADGEN · Transcription factor binding sites (TFBSs)
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