Specific DNA recognition by theAntp homeodomain: MD simulations of specific and nonspecific complexes

How DNA affects the hyperthermophilic protein Ape10b2 for oligomerization: an investigation using multiple short molecular dynamics simulations

Alba2 is a hyperthermophilic DNA-binding protein, and DNA plays a crucial role in the Alba2 oligomerization process. It is a pity that there is limited research in terms of how DNA affects the conformational change of Alba2 in oligomerization. Herein, we complement the crystal structure of the Ape10b2 (belongs to Alba2)-dsDNA complex (PDB ID: 3U6Y) and employ multiple short molecular dynamics (MSMD) simulations to illuminate the influence of DNA on Ape10b2 at four temperatures (300, 343, 363, and 373 K). Our results indicate that DNA could cause the conformational changes of two important regions (loop1 and loop5), which may be beneficial for protein oligomerization. The results of hydrogen bond analysis show that the increasing number of hydrogen bonds between two monomers of Ape10b2 may also be a favorable factor for oligomerization. In addition, Ape10b2 can stabilize DNA by electrostatic interactions with an increase in temperature, and five residues (Arg40, Arg42, Asn43, Asn45, and Arg46) play a stabilizing role during protein binding to DNA. Our findings could help in understanding the favorable factors leading to protein oligomerization, which contributes to enzyme engineering research from an industrial perspective.

Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations

An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is the loss of entropy that occurs from restricting the conformational freedom of amino acid side chains. The effect of restricting the flexibility of several side chains at a protein-DNA interface may be comparable in many cases to the other factors that determine the binding thermodynamics and may, therefore, play a key role in dictating the binding affinity and/or specificity. Because the entropic contributions, including the presence and influence of side-chain dynamics, are especially difficult to estimate based on structural information, it is important to pursue experimental and theoretical studies that can provide direct information regarding these issues. We report on studies of a model system, the homeodomain/DNA complex, focusing on the Lys50 class of homeodomains where a key lysine residue in position 50 was shown previously to be critical for binding site specificity. NMR methodology was employed for determining the dynamics of lysine side-chain amino groups via 15N relaxation measurements in the Lys50-class homeodomains from the Drosophila protein Bicoid and the human protein Pitx2. In the case of Pitx2, complexes with both a consensus and a nonconsensus DNA binding site were examined. NMR-derived order parameters indicated moderate to substantial conformational freedom for the lysine NH3+ group in the complexes studied. To complement the experimental NMR measurements, molecular dynamics simulations were performed for the consensus complexes to gain further, detailed insights regarding the dynamics of the Lys50 side chain and other important residues in the protein-DNA interface.

Interaction of classical platinum agents with the monomeric and dimeric Atox1 proteins: a molecular dynamics simulation study

We carried out molecular dynamics simulations and free energy calculations for a series of binary and ternary models of the cisplatin, transplatin and oxaliplatin agents binding to a monomeric Atox1 protein and a dimeric Atox1 protein to investigate their interaction mechanisms. All three platinum agents could respectively combine with the monomeric Atox1 protein and the dimeric Atox1 protein to form a stable binary and ternary complex due to the covalent interaction of the platinum center with the Atox1 protein. The results suggested that the extra interaction from the oxaliplatin ligand-Atox1 protein interface increases its affinity only for the OxaliPt + Atox1 model. The binding of the oxaliplatin agent to the Atox1 protein might cause larger deformation of the protein than those of the cisplatin and transplatin agents due to the larger size of the oxaliplatin ligand. However, the extra interactions to facilitate the stabilities of the ternary CisPt + 2Atox1 and OxaliPt + 2Atox1 models come from the α1 helices and α2-β4 loops of the Atox1 protein-Atox1 protein interface due to the cis conformation of the platinum agents. The combinations of two Atox1 proteins in an asymmetric way in the three ternary models were analyzed. These investigations might provide detailed information for understanding the interaction mechanism of the platinum agents binding to the Atox1 protein in the cytoplasm.

Binding polymorphism in the DNA bound state of the Pdx1 homeodomain

The subtle effects of DNA-protein recognition are illustrated in the homeodomain fold. This is one of several small DNA binding motifs that, in spite of limited DNA binding specificity, adopts crucial, specific roles when incorporated in a transcription factor. The homeodomain is composed of a 3-helix domain and a mobile N-terminal arm. Helix 3 (the recognition helix) interacts with the DNA bases through the major groove, while the N-terminal arm becomes ordered upon binding a specific sequence through the minor groove. Although many structural studies have characterized the DNA binding properties of homeodomains, the factors behind the binding specificity are still difficult to elucidate. A crystal structure of the Pdx1 homeodomain bound to DNA (PDB 2H1K) obtained previously in our lab shows two complexes with differences in the conformation of the N-terminal arm, major groove contacts, and backbone contacts, raising new questions about the DNA recognition process by homeodomains. Here, we carry out fully atomistic Molecular Dynamics simulations both in crystal and aqueous environments in order to elucidate the nature of the difference in binding contacts. The crystal simulations reproduce the X-ray experimental structures well. In the absence of crystal packing constraints, the differences between the two complexes increase during the solution simulations. Thus, the conformational differences are not an artifact of crystal packing. In solution, the homeodomain with a disordered N-terminal arm repositions to a partially specific orientation. Both the crystal and aqueous simulations support the existence of different stable binding conformers identified in the original crystallographic data with different degrees of specificity. We propose that protein-protein and protein-DNA interactions favor a subset of the possible conformations. This flexibility in DNA binding may facilitate multiple functions for the same transcription factor.

Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis

Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.

Structural effect of the L16Q, K50E, and R53P mutations on homeodomain of pituitary homeobox protein 2

The transcription factor pituitary homeobox protein 2 (PITX2) is involved in genetic control of development. Mutations in PITX2, most in the homeodomain, cause the autosomal-dominant disorder Rieger syndrome. The mutants L16Q, K50E and R53P destabilize the structure and disrupt DNA-binding activity. The biological functions of these mutants have been characterized but not the structural basis behind the loss of DNA-binding activity. We performed multiple molecular dynamics simulations at 37°C to investigate the structural and dynamic effects of the 3 PITX2 homeodomain mutants. Compared with the wild type (WT), the L16Q mutant induces a kink in the α3 helix, which is stabilized by the hydrogen bond of Q21-R59. The disruption in backbone hydrogen bonds of V47-N51 and W48-R52 leads to a kink formation in the α3 helix of K50E. The R53P mutant alters the relative orientation of helices, which is apparently stabilized by the formation of new hydrogen bonds of T38-Q11, T38-Q12, T38-R2, N39-R2, L40-Q1, L40-R2, and T41-Q4. The hydrophobic core residues F8, L13, L40 and V45 change their positions in all mutants to break the hydrophobic core. Thus, changes in helical orientations and hydrophobic core cause rearrangement of the DNA-binding surface and disrupt DNA-binding activity in the mutants. The structural and molecular dynamics properties of 3 PITX2 homeodomain mutants differ from those of the WT, especially in formation of a kink in the recognition helix, change in the packing of helices and disruption of the hydrophobic core. This structural basis for the loss of DNA-binding activity for these polymorphisms may help in understanding the effect of mutations on other homeodomains with other diseases.

Roles for intrinsic disorder and fuzziness in generating context-specific function in Ultrabithorax, a Hox transcription factor

Surprisingly few transcription factors drive animal development relative to the number and diversity of final tissues and body structures. Therefore, most transcription factors must function in more than one tissue. In a famous example, members of the Hox transcription factor family are expressed in contiguous stripes along the anterior/posterior axis during animal development. Individual Hox transcription factors specify all tissues within their expression domain and thus must respond to cellular cues to instigate the correct tissue-specific gene regulatory cascade. We describe how, in the Drosophila Hox protein Ultrabithorax, intrinsically disordered regions implement, regulate and co-ordinate multiple functions, potentially enabling context-specific gene regulation. The large N-terminal disordered domain encodes most of the transcription activation domain and directly impacts DNA binding affinity by the Ubx homeodomain. Similarly, the C-terminal disordered domain alters DNA binding affinity and specificity, interaction with a Hox binding protein and strongly influences both transcription activation and repression. Phosphorylation of the N-terminal disordered domain and alternative splicing of the C-terminal disordered domain could allow the cell to both regulate and co-ordinate DNA binding, protein interactions and transcription regulation. For regulatory mechanisms relying on disorder to continue to be available when Ubx is bound to other proteins or DNA, fuzziness would need to be preserved in these macromolecular complexes. The intrinsically disordered domains in Hox proteins are predicted to be on the very dynamic end of the disorder spectrum, potentially allowing disorder to persist when Ubx is bound to proteins or DNA to regulate the function of these "fuzzy" complexes. Because both intrinsically disordered regions within Ubx have multiple roles, each region may implement several different regulatory mechanisms identified in fuzzy complexes. These intrinsic disorder-based regulatory mechanisms are likely to be critical for allowing Ubx to sense tissue identity and respond by implementing a context-specific gene regulatory cascade.

Interaction identification of Zif268 and TATA(ZF) proteins with GC-/AT-rich DNA sequence: A theoretical study

Molecular dynamics (MD) simulations for Zif268 (a zinc-finger-protein binding specifically to the GC-rich DNA)-d(A(1) G(2) C(3) G(4) T(5) G(6) G(7) G(8) C(9) A(10) C(11) )(2) and TATA(ZF) (a zinc-finger-protein recognizing the AT-rich DNA)-d(A(1) C(2) G(3) C(4) T(5) A(6) T(7) A(8) A(9) A(10) A(11) G(12) G(13) )(2) complexes have been performed for investigating the DNA binding affinities and specific recognitions of zinc fingers to GC-rich and AT-rich DNA sequences. The binding free energies for the two systems have been further analyzed by using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The calculations of the binding free energies reveal that the affinity energy of Zif268-DNA complex is larger than that of TATA(ZF) -DNA one. The affinity between the zinc-finger-protein and DNA is mainly driven by more favorable van-der-Waals and nonpolar/solvation interactions in both complexes. However, the affinity energy difference of the two binding systems is mainly caused by the difference of van-der-Waals interactions and entropy components. The decomposition analysis of MM-PBSA free energies on each residue of the proteins predicts that the interactions between the residues with the positive charges and DNA favor the binding process; while the interactions between the residues with the negative charges and DNA behave in the opposite way. The interhydrogen-bonds at the protein-DNA interface and the induced intrafinger hydrogen bonds between the residues of protein for the Zif268-DNA complex have been identified at some key contact sites. However, only the interhydrogen-bonds between the residues of protein and DNA for TATA(ZF) -DNA complex have been found. The interactions of hydrogen-bonds, electrostatistics and van-der-Waals type at some new contact sites have been identified. Moreover, the recognition characteristics of the two studied zinc-finger-proteins have also been discussed.

20ns molecular dynamics simulation of the antennapedia homeodomain-DNA complex: water interaction and DNA structure analysis

Homeodomains are one of the important families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. The crystal structure and NMR structure of the antennapedia homeodomain-DNA complex and comparison between them is available. Although earlier works have shown that the direct contacts and water mediated contacts are important for the binding and specificity. The detail dynamical structural characteristics of the complex, water mediating interactions in the complex and also the detail study of the free DNA and protein has not done. In the present paper we have reported the results of 20ns MD simulation of this complex with the presence of explicit water and also the 20ns MD simulation of the protein and the DNA separately in explicit water. The results show that the complex remains stable during the last 8ns of the simulation. The part of the protein which is interacting with the DNA has fewer fluctuations than other part of the protein. The pattern of water distribution around the interacting center has a typical pattern for this complex and it is quite different from the free protein and the free DNA. Water molecules penetrate into the interacting center during the simulation. Several water bridges have been identified which is responsible for recognition but not observed in the crystal structure. The recognized DNA sequence (14 mer) has been characterized by helical and step parameters. The correlated motions of the DNA and the protein in the complexed form and the free form has been analyzed.

Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: a molecular dynamics study

Molecular dynamics simulations and free energy calculations have been performed on the transcription factor Ndt80 either in complex with the native DNA sequence or with a mutant DNA with a switched central base pair, C5-G5' to G5-C5'. This mutant has been shown to have a 100-fold decrease in binding affinity of Ndt80, and in this study we explain this both structurally and energetically. The major interactions between the protein and the DNA were maintained in the simulations, apart from around the mutation site. The crystal structure of the Ndt80-DNA complex revealed that R177 makes a base specific bidentate interaction with G5' which is part of a conserved 5'-YpG-3' step. In the simulation with the mutant DNA, the side chain of R177 changes conformation and makes three new stable hydrogen bonds to the DNA backbone. This in turn induces a conformational change in the DNA backbone of the T6'-G5' step from the unusual BII state to the canonical BI state. The affinity difference for the protein-DNA complex with the native DNA compared with the mutant DNA is only about 3 kcal/mol. The free energy calculations of the base pair switch indicated a larger difference than what was found experimentally, about 7.7 kcal/mol, but this is explained in structural terms using the 10 ns simulations of the solvated complexes and the rearrangement of the R177 side chain.

Conformational stability and DNA binding energetics of the rat thyroid transcription factor 1 homeodomain

The conformational stability of the rat thyroid transcription factor 1 homeodomain, TTF-1HD, has been investigated by means of circular dichroism (CD) and differential scanning calorimetry (DSC) measurements at pH 5.0 as a function of KCl concentration. Thermal unfolding of TTF-1HD is a reversible two-state transition. The protein is not stable against temperature, showing a denaturation temperature of 32 degrees C in the absence of salt and 50 degrees C at 75 mM KCl. The binding energetics of TTF-1HD to its target DNA sequence has been characterized by means of isothermal titration calorimetry (ITC) measurements, complemented with CD data. At 25 degrees C, pH 5.0 and 75 mM KCl, the binding constant amounts to 1.5 x 10(8)M(-1) and the binding enthalpy change amounts to -41 kJ mol(-1). The process is enthalpy driven, but also the entropy change is favorable to complex formation. To gain a molecular level understanding of the interactions determining the association of TTF-1HD to the target DNA sequence structural information would be requested, but it is not yet available. Therefore, structural models of two complexes, TTF-1HD with the target DNA sequence and TTF-1HD with a modified DNA sequence, have been constructed by using as a template the NMR structure of the complex between NK-2 HD and its target DNA, and by performing molecular dynamics simulations 3.5 ns long. Analysis of these models allows one to shed light on the origin of the DNA binding specificity characteristic of TTF-1HD.

A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations

A properly identified transition state ensemble (TSE) in a molecular dynamics (MD) simulation can reveal a tremendous amount about how a protein folds and offer a point of comparison to experimentally derived Phi(F) values, which reflect the degree of structure in these transient states. In one such method of TSE identification, dubbed P(fold), MD simulations of individual protein structures taken from an unfolding trajectory are used to directly assess an input structure's probability of folding before unfolding, and P(fold) is, by definition, 0.5 for the TSE. Other, less computationally intensive methods, such as multidimensional scaling (MDS) of the pairwise root mean-squared deviation (RMSD) matrix of the conformations sampled in a thermal unfolding trajectory, have also been used to identify the TSE. Identification of the TSE is made from the original MD simulation without the need to run further simulations. Here we present a P(fold)-like study and describe methods for identification of the TSE through the derivation of a high fidelity, bounded, one-dimensional reaction coordinate for protein folding. These methods are applied to the engrailed homeodomain. The TSE identified by this approach is essentially identical to the TSE identified previously by MDS of the pairwise RMSD matrix. However, the cost of performing P(fold), or even our reduced P(fold)-like calculations, is at least 36,000 times greater than the MDS method.

Decoding transcriptional regulatory interactions

Transcription factor proteins control the temporal and spatial expression of genes by binding specific regulatory elements, or motifs, in DNA. Mapping a transcription factor to its motif is an important step towards defining the structure of transcriptional regulatory networks and understanding their dynamics. The information to map a transcription factor to its DNA binding specificity is in principle contained in the protein sequence. Nevertheless, methods that map directly from protein sequence to target DNA sequence have been lacking, and generation of regulatory maps has required experimental data. Here we describe a purely computational method for predicting transcription factor binding. The method calculates the free energy of binding between a transcription factor and possible target DNA sequences using thermodynamic integration. Approximations of additivity (each DNA basepair contributes independently to the binding energy) and linear response (the DNA-protein and DNA-solvent couplings are linear in an effective reaction coordinate representing the basepair character at a specific position) make the computations feasible and can be verified by more detailed simulations. Results obtained for MAT-alpha2, a yeast homeodomain transcription factor, are in good agreement with known results. This method promises to provide a general, computationally feasible route from a genome sequence to a gene regulatory network.

The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site

The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in addition, the Bcd homeodomain can recognize an array of different DNA sites. The dual functionality and broad recognition capabilities signify that the Bcd homeodomain may possess unique structural/dynamic properties. Bicoid is the founding member of the K50 class of homeodomain proteins, containing a lysine residue at the critical 50th position (K50) of the homeodomain sequence, a residue required for DNA and RNA recognition; Bcd also has an arginine residue at the 54th position (R54), which is essential for RNA recognition. Bcd is the only known homeodomain with the K50/R54 combination of residues. The Bcd structure indicates that this homeodomain conforms to the conserved topology of the homeodomain motif, but exhibits a significant variation from other homeodomain structures at the end of helix 1. A key result is the observation that the side-chains of the DNA-contacting residues K50, N51 and R54 all show strong signs of flexibility in the protein-DNA interface. This finding is supportive of the adaptive-recognition theory of protein-DNA interactions.

Homology modeling based solution structure of Hoxc8-DNA complex: role of context bases outside TAAT stretch

The 3D structure of neither Hoxc8 nor Hoxc8-DNA complex is known. The repressor protein Hoxc8 binds to the TAAT stretch of the promoter of the osteopontin gene and modulates its expression. Over expression of the osteopontin gene is related to diseases like osteoporosis, multiple sclerosis, cancer et cetera. In this paper we have proposed a 3D structure of Hoxc8-DNA complex obtained by Homology modeling and molecular dynamics (MD) simulation in explicit water. The crystal structure (9ant.pdb) of Antennapedia homeodomain in complex with its DNA sequence was chosen as the template based on (i) high sequence identity (85% for the protein and 60% for the DNA) and (ii) the presence of the TAAT stretch in interaction with the protein. The resulting model was refined by MD simulation for 2.0ns in explicit water. This refined model was then characterized in terms of the structural and the interactional features to improve our understanding of the mechanism of Hoxc8-DNA recognition. The interaction pattern shows that the residues Ile(195), Gln(198), and Asn(199), and the bases S2-(4)TAATG(8) are most important for recognition suggesting the stretch TAATG as the "true recognition element" in the present case. A strong and long-lived water bridge connecting Gln(198) and the base of S1-C(7) complementary to S2-G(8) was observed. Our predicted model of Hoxc8-DNA complex provides us with features that are consistent with the available experimental data on Hoxc8 and the general features of other homeodomain-DNA complexes. The predictions based on the model are also amenable to experimental verification.