Performed MD Simulations Research Articles

Do Columns of Azobenzene Stars Disassemble under Light Illumination?

The clustering properties of star-shaped molecules comprising three photochromic azobenzene-containing arms are investigated with specific focus on the influence of light on these structures. Previous experimental works report self-assembly of azobenzene stars in aqueous solution into long columnar clusters that are detectable using optical microscopy. These clusters appear to vanish under UV irradiation, which is known to induce trans-to-cis photoisomerization of the azobenzene groups. We have performed MD simulations, density functional theory, and density functional tight binding calculations to determine conformational properties and binding energies of these clusters. Our simulation data suggest that the binding strength of the clusters is large enough to prevent a breaking along their main axis. We conclude that very likely other mechanisms lead to the apparent disappearance of the clusters.

Characteristics of atomic elastic stiffness at GSF energy surface, edge and screw dislocation cores in fcc, bcc and hcp metals

Basic characteristics of 6 × 6 matrix of atomic elastic stiffness (AES), Bija=Δσia/Δεj, or the deformation resistance at each atom point, are discussed first in static analyses of generalized stacking fault (GSF) energy surface for 8 fcc, 4 bcc and 4 hcp metals with Zhou’s EAM potential. For hcp metals, the stress–strain peak along the GSF path exactly coincides with the point where the AES loses the resistance showing negative 1st eigenvalue ηa(1), or the solution of BijaΔεj=ηaΔεi=Δσia; however, all fcc and 2 bcc (Mo and W) never have negative ηa(1) along the GSF path. Fe and Ta transiently show ηa(1) < 0 while they also have positive ηa(1) at the GSF energy peak. Then we performed MD simulations of edge and screw dislocation dipoles in a periodic slab cell of typical elements of fcc, bcc and hcp; and discussed the eigenvalue and the corresponding eigenvector {Δεxx, Δεyy, Δεzz, Δγyz, Δγzx, Δγxy} of the dislocation cores. As expected from the results of the GSF analyses, dislocation cores in fcc Ni have no ηa(1) < 0 atoms, even in their glide process under external shear loading. Bcc Fe and hcp Co definitely have ηa(1) < 0 atoms in the dislocation cores and their migration direction can be visualized by the maximum shear direction of the strain tensor of the corresponding eigenvector.

Structural insight into the serotonin (5-HT) receptor family by molecular docking, molecular dynamics simulation and systems pharmacology analysis.

Serotonin (5-HT) receptors are proteins involved in various neurological and biological processes, such as aggression, anxiety, appetite, cognition, learning, memory, mood, sleep, and thermoregulation. They are commonly associated with drug abuse and addiction due to their importance as targets for various pharmaceutical and recreational drugs. However, due to a high sequence similarity/identity among 5-HT receptors and the unavailability of the 3D structure of the different 5-HT receptor, no report was available so far regarding the systematical comparison of the key and selective residues involved in the binding pocket, making it difficult to design subtype-selective serotonergic drugs. In this work, we first built and validated three-dimensional models for all 5-HT receptors based on the existing crystal structures of 5-HT1B, 5-HT2B, and 5-HT2C. Then, we performed molecular docking studies between 5-HT receptors agonists/inhibitors and our 3D models. The results from docking were consistent with the known binding affinities of each model. Sequentially, we compared the binding pose and selective residues among 5-HT receptors. Our results showed that the affinity variation could be potentially attributed to the selective residues located in the binding pockets. Moreover, we performed MD simulations for 12 5-HT receptors complexed with ligands; the results were consistent with our docking results and the reported data. Finally, we carried out off-target prediction and blood-brain barrier (BBB) prediction for Captagon using our established hallucinogen-related chemogenomics knowledgebase and in-house computational tools, with the hope to provide more information regarding the use of Captagon. We showed that 5-HT2C, 5-HT5A, and 5-HT7 were the most promising targets for Captagon before metabolism. Overall, our findings can provide insights into future drug discovery and design of medications with high specificity to the individual 5-HT receptor to decrease the risk of addiction and prevent drug abuse.

Critical Contact Angle to Induce Capillary Rise of Polymers in Nanopores Does Not Depend on Chain Length.

We study the effect of physical confinement on the capillary infiltration of polymers into cylindrical nanopores using molecular dynamics simulations. In particular, we probe whether the critical contact angle (θc) above which capillary rise infiltration ceases to occur changes for long-chain polymers, possibly due to loss of conformation entropy induced by chain confinement. Surprisingly, θc does not strongly depend on the length of polymer chains and stays constant for large N. A free energy model is developed to show that θc depends strongly on the size of statistical segments rather than N, which we confirm by performing MD simulations of infiltration with semiflexible polymers. These results could provide guidelines in manufacturing polymer nanostructures and nanocomposites using capillary rise infiltration.

Spontaneous transitions of actin-bound tropomyosin toward blocked and closed states.

After muscle contraction, myosin cross-bridge heads detach from thin actin filaments during relaxation. Structural and kinetic data of cross-bridge-thin filament interactions have shown that tropomyosin's position on F-actin is biased toward the blocked or closed states when myosin detaches. It is not clear if structural linkages between tropomyosin and myosin cross-bridge heads, or tropomyosin and Ca2+-free troponin, drive the process or whether tropomyosin movement is energetically independent of myosin and troponin influence. Here we provide in silico data about tropomyosin dynamics on troponin/myosin-free F-actin indicating that tropomyosin moves from the open state toward blocked- or closed-state positions on actin. To follow transitions inherent to tropomyosin itself on F-actin, we performed MD simulations initiated from the blocked-, open-, and intermediate-state models and followed tropomyosin over the surface of F-actin in the absence of myosin and troponin. These MD simulations maintain tropomyosin in a cable-like conformation, including the tropomyosin overlap domain, while allowing tropomyosin to retain most of its motional freedom. Tropomyosin shows considerable azimuthal movement away from the open state toward the surrounds of a more energetically favorable blocked B-state position over F-actin. In contrast, little movement away from the B-state location is observed. Our results are consistent with previous predictions based on electrostatic interaction energy landscapes determined by rigid-body translocation of tropomyosin. They support the view that in the absence of myosin, i.e., when myosin cross-bridges detach from actin, the blocked- or closed-state positions of tropomyosin are energetically favored, while the open state is not.

An evaluation of the structures of cellulose generated by the CHARMM force field: comparisons to in planta cellulose

Molecular dynamics simulations of cellulose regularly sample a conformational space different to the crystal structures they were initiated from, with changes to the tilt of chains, expansion of the unit cell and variation in exocyclic group conformations. Given the differences in the structures sampled the question presents itself as to whether these simulations are sampling structures that resemble cellulose in planta. To investigate this question, we have performed MD simulations on different size and shaped Iα and Iβ cellulose microfibrils with the structures generated characterized with regards to changes in expansion, chain shift along the polymerization axis, tilt, exocyclic conformation and H-bonding. Structures were then input into a quantum mechanical NMR chemical shift calculation protocol with the resulting 13C chemical shifts compared to experimental data. Chemical shifts were shown to be strongly dependent on the exocyclic group conformation with the structures of Iα simulations more closely replicating experimental data than the Iβ simulations, especially at the C4 and C6 positions which suggests that the conformational space was not being accurately represented for the Iβ microfibrils. Despite this, peak sizes based on the sampling occupancy of exocyclic conformations from unrestrained simulations were found to replicate experimental peak sizes better than simulations where exocyclic groups of interior chains were restrained to the tg conformation, suggesting that exocyclic groups have greater freedom to sample different conformations than suggested by their crystal structures.

Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel

The epithelial sodium channel (ENaC) mediates sodium absorption in lung, kidney, and colon epithelia. Channels in the ENaC/degenerin family possess an extracellular region that senses physicochemical changes in the extracellular milieu and allosterically regulates the channel opening. Proteolytic cleavage activates the ENaC opening, by the removal of specific segments in the finger domains of the α- and γ ENaC-subunits. Cleavage causes perturbations in the extracellular region that propagate to the channel gate. However, it is not known how the channel structure mediates the propagation of activation signals through the extracellular sensing domains. Here, to identify the structure-function determinants that mediate allosteric ENaC activation, we performed MD simulations, thiol modification of residues substituted by cysteine, and voltage-clamp electrophysiology recordings. Our simulations of an ENaC heterotetramer, α1βα2γ, in the proteolytically cleaved and uncleaved states revealed structural pathways in the α-subunit that are responsible for ENaC proteolytic activation. To validate these findings, we performed site-directed mutagenesis to introduce cysteine substitutions in the extracellular domains of the α-, β-, and γ ENaC-subunits. Insertion of a cysteine at the α-subunit Glu557 site, predicted to stabilize a closed state of ENaC, inhibited ENaC basal activity and retarded the kinetics of proteolytic activation by 2-fold. Our results suggest that the lower palm domain of αENaC is essential for ENaC activation. In conclusion, our integrated computational and experimental approach suggests key structure-function determinants for ENaC proteolytic activation and points toward a mechanistic model for the allosteric communication in the extracellular domains of the ENaC/degenerin family channels.

A Molecular Dynamics Study on the Self-Assembly of Supramolecular Nanotubule

Self-assembly of peptide-based building blocks has been shown to be useful in constructing artificial bionanostructures. Recently, a rational approach to construct â-barrel protein mimics from the self-assembly of peptide-based building blocks has been demonstrated. In recent experiments, diverse novel supramolecular nanotubules are prepared by adopting non-covalent bonding amphiphiles as the building block to mimic these biological structures. We performed MD simulations on the proposed nanoring structures formed by the self-assembly of â-sheet forming peptides. The stability of the nanoring structure with respect to the size is investigated and several factors contributing to the stability are examined. We have also demonstrated that the sizes of nanorings can be controlled by introducing selective mutations. We also performed molecular dynamics simulation on self-assembled supramolecular nanotubule constructed by bent-shaped rod amphiphile as a building block. By systematically examining from small aggregate composed of several molecules to fully constructed toroidal shape, we identified optimal structure consistent with experimental data. We illustrated that cooperative contributions of various interactions play a role as a driving force to construct a nanotubule from small fragmental intermediates. Understanding strategies for rational designs of such structures will be discussed.

Dissecting the Forces that Dominate Dimerization of the Nucleotide Binding Domains of ABCB1

P-glycoprotein, also known as multidrug resistance protein 1 or ABCB1, can export a wide range of chemically unrelated compounds, including chemotherapeutic drugs. ABCB1 consists of two transmembrane domains that form the substrate binding and translocation domain, and of two cytoplasmic nucleotide binding domains (NBDs) that energize substrate transport by ATP binding and hydrolysis. ATP binding triggers dimerization of the NBDs, which switches the transporter from an inward facing to an outward facing transmembrane domain conformation. We performed MD simulations to study the dynamic behavior of the NBD dimer in the presence or absence of nucleotides. In the apo configuration, the NBDs were overall attractive to each other as shown in the potential of mean force profile, but the energy well was shallow and broad. In contrast, a sharp and deep energy minimum (∼−42 kJ/mol) was found in the presence of ATP, leading to a well-defined conformation. Motif interaction network analyses revealed that ATP stabilizes the NBD dimer by serving as the central hub for interdomain connections. Simulations showed that forces promoting dimerization are multilayered, dominated by electrostatic interactions between the nucleotide and conserved amino acids of the signature sequence and the Walker A motif. In addition, direct and water-bridged hydrogen bonds between NBDs provided conformation-defining interactions. Importantly, we characterized a largely unrecognized but essential contribution from hydrophobic interactions between the adenine moiety of the nucleotides and a hydrophobic surface of the X-loop to the stabilization of the nucleotide-bound NBD dimer. These hydrophobic interactions lead to a sharp energy minimum, thereby conformationally restricting the nucleotide-bound state.

Molecular dynamics of a far positioned SOD1 mutant V14M reveals pathogenic misfolding behavior

Human superoxide dismutase (Cu/Zn SOD1) is a homodimeric enzyme. Mutations in Cu/Zn SOD1 causes a familial form of amyotrophic lateral sclerosis (fALS), and aggregation of mutant SOD1 has been proposed to play a role in neurodegeneration. Though a majority of the mutations are point substitutions, there are a few changes that result in amino acid deletions or truncations of the polypeptide. These pathogenic mutations are scattered throughout the three-dimensional structure of the dimeric enzyme, which creates a puzzling pattern to investigate the molecular determinants of fALS. The most common hypothesis proposed that the misfolding of SOD1 mutants are primarily triggered by decreased affinity for metal ions. However, this hypothesis is challenging, as a significant number of disease-causing mutations are located far away from the metal-binding site and dimer interface. So in the present study, we have investigated the influence of such a far positioned pathogenic mutation, V14M, in altering the stability and folding of the Cu/Zn SOD1. Though the location of Val14 is far positioned, it has a vital role in the stability of SOD1 by preserving its hydrophobic cluster at one end of the β barrel domain. We have performed MD simulations of the V14M mutant for 80 ns timescale. The results reveal the fact that irrespective of its location, V14M mutation triggers a conformational change that is more similar to that of the metal-deficient holo form and could resemble an intermediate state in the folding reaction which results in protein misfolding and aggregation.

Improvement of molecular dynamics simulation method applied to nematics doped with racemic metal complexes

ABSTRACTIn order to carry out MD simulations for the racemic system consisting of two different enantiomers of a chiral ruthenium complex and nematic liquid crystal molecules accurately, we here proposed modified force field parameters for the chiral dopant. The validity of the modified parameter was confirmed by performing MD simulations for pure ruthenium complex system at crystalline state. MD simulations for the racemic system of Δ- and Λ-isomers of the chiral dopant molecule and nematic solvent molecules led to the accurate and precise determination of the helical twisting power of the chiral dopant.

C-1311 (Symadex), a potential anti-cancer drug, intercalates into DNA between A and G moieties. NMR-derived and MD-refined stereostructure of the d(GAGGCCTC)2:C-1311 complex

Imidazoacridinone C-1311 (Symadex®) is an antitumor agent which has been recommended for Phase II clinical trials a few years ago. Previously, it was shown experimentally that during the initial stage of its action C-1311 forms stable intercalation complexes with DNA duplexes. Herein, a NMR-derived stereostructure of d(GAGGCCTC)2:C-1311 complex was reported. The ligand was found locating itself between A and G moieties, forming symmetrical DNA:drug 1:2 mol/mol complex. Intercalation site was located upon the DNA-ligand proton/proton dipolar couplings observed in the NOESY spectrum and the performed MD simulations. NMR-derived stereostructure was hence refined by restrained MD using distance restraints obtained from the NOESY data and the result was compared with MD-derived structure of the proposed complex, obtained from the calculations performed with distance restraints applied only for hydrogen bonds in the terminal GC base pairs. The results of both simulations were coherent. Basing on the observed C-1311's intercalation sites and on our previous results concerning the d(CGATCG)2:C-1311 complex, we stated that AG/GA sequences are the preferred binding sites of imidazoacridinone C-1311.

Unconventional Ion-Permeation Pathways in NaVAb and CavAb Channels from Molecular Simulations with Polarizable Force-Fields

The availability of high-resolution structures for bacterial homologuesvariety of well-established force-fields firmly established that selective Na+ transport relies on the multi-ion permeation mechanisms with some substantial differences from a narrow-pore knock-on permeation detailed for K+ selective channels. However, binding of multiple ions into a crowded space common to selectivity filters pose a number of conceptual questions regarding role of local of Na+ and Ca2+ selective channels open an avenue for in-depth understanding of selective permeation mechanisms central to electrical signaling in excitable cells. A plethora of studies performed with classical Molecular Dynamics simulations techniques using a dielectric and polarization effects. Our recent work firmly established limits of applicability of the classical force-fields in studies of divalent ions binding to metalloprotein hosts. The energetics of Na+ interactions with protein hosts is captured considerably better by classical approximation. To establish detailed permeation mechanisms with explicit account for polarization effects, we performed MD simulations combined with QM computations for different mixtures of sodium, potassium, calcium ions permeating across Na+ selective (NaVAb) and Ca2+ selective (CavAb), channels. From 2D PMFs and QM ion-protein interaction energies, we reported significant changes in the permeation pathways of ions in these two models unravelling bases of selective transport in physiologically relevant ion channels. We proposed a different view on how the channels select ions, in a way that is clearly distinguishable from potassium-selective channels.

Improved CHARMM Additive Force Field Parameters to Accurately Model Tyrosine-Choline Cation-π Interactions

Cation-π interactions between methylated ammonium groups and tyrosine amino acids have been shown to be important for epigenetic recognition motifs, choline-binding proteins, and for protein-lipid interactions. Accurately modeling cation-π interactions in biomolecular simulations remains a challenge due to the lack of explicit polarization or charge transfer effects. In this work, we investigate the nature of tyrosine-choline cation-π interactions by performing high-level Quantum Mechanical (QM) calculations and building Potential Energy Surfaces (PES). We benchmark QM levels of theory and find that SAPT2+/aug-cc-pVDZ level of theory performs well compared to large basis set CCSD(T). Further, we compared QM PES (using SAPT2+/aug-cc-pVDZ) to both additive CHARMM36 and Drude polarizable force field. With CHARMM36, the equilibrium distances are well captured while the interaction energies are underestimated for various approach angles of TMA with respect to phenol. While using the Drude polarizable force field, the interaction energies deviate less compared to target QM data. However, the obtained equilibrium geometries are slightly underestimated. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones potentials for selected atom pairs involved in phenol-TMA cation-π interactions. We performed MD simulations of a bilayer-bound bacterial phospholipase and calculate the occupancies of tyrosine-choline cation-π interactions. The cation-π occupancies obtained with the modified set correlate better with experimental data than those obtained with the CHARMM force field.

MD Simulations and CD Spectroscopies of (Benz)Acridine: rDNA G-Quadruplex Complexes

In both prokaryotic and eukaryotic cells, guanine-rich stretches of DNA sequences are found in gene regulatory regions and telomeric DNAs to form G-quadruplexes, and they are involved in many fundamental biological processes and have been implicated in a number of diseases including cancer. While most previous G-quadruplex studies have focused on telomeric G-quadruplexes for validating targets for anticancer therapy, the nucleolar G-quadruplexes may be an even more promising target for chemotherapeutic intervention. The nucleolus plays a central role in tumor pathology because it controls the high level of ribosomal RNA (rRNA) synthesis necessary to sustain ribosome biogenesis during rapid cancer cell growth. Ribosome biogenesis occurs in the nucleolus and is tightly regulated by many cell signaling pathways that converge on the RNA polymerase I complex (Pol I). Using small molecules (drugs) to disrupt ribosome biogenesis represents an attractive strategy for selectively killing cancer cells. Aromatic acridines that sit on top of a G-quadruplex tetrad via π-π stacking interactions have been extensively explored as scaffolds for developing G-quadruplex-specific binders. In this present study, we performed MD simulations of 13 modeled putative rDNA G-quadruplexes that have been characterized via CD spectra to form G-quadruplexes. In addition, we simulated their interactions with designed acridines and benzacridines and analyzed them using a set of novel order parameters to quantify their binding selectivities. We are currently validating our computational predictions via CD spectra. In one G-quadruplex we studied, NUC 23, CD spectra shows that it adopts a parallel topology structure that is further stabilized upon interactions with benzacridine. In excellent agreement, we also observe the same phenomenon in our MD simulations.

Molecular Dynamics Analysis on the Force Transmission Pathway via Inter-Subunit Pathway for Mechano-Gating of Bacterial Mechanosensitive Channel MscL

The bacterial mechanosensitive channel MscL is constituted of homopentamer of a subunit with TM1 inner and TM2 outer transmembrane helix. The major issue on MscL is to understand the gating mechanism driven by membrane tension. Upon membrane stretch, the helices are dragged by lipids at the tension sensor F78 and tilted, accompanied by outward sliding, leading to a gate expansion. To get insights into the relationship between F78 and the gate including G22, we performed MD simulations of G22N GOF and F78N LOF MscLs and G22N showed spontaneous opening without membrane stretch, while F78N could not be opened even under strong membrane tension.

Molecular Dynamics Study of Fluid Solid Interfacial Slip and Its Effect on Aerodynamic Drag

Interfacial hydrodynamic slippage is controlled by two factors say physical structure and chemical composition. Various studies have been conducted experimentally which try to connect the physical structure of the surface and its chemical property on the interfacial wettability. One such example is the Tunable wettability in surface-modified ZnO-based hierarchical nanostructures [2]. In which vertically aligned Nanoneedles and Nanonails were employed as a platform to determine the effect of surface structure. According to which a variation in static contact angles were observed as the cap size the nanonails constantly increased. Starting with a contact angle of 104° the contact angle first increases and then decreases, which means that the slip length first increases and then decreases. The increase in slip length reduces the drag, which has immense application in the aerodynamic field. This paper investigates the relation between the chemical wettability and aerodynamic drag by performing MD simulations of couette flow with varying fluid-surface interaction.

The electronic density obtained from a QTAIM analysis used as molecular descriptor. A study performed in a new series of DHFR inhibitors

The results reported here indicate that the electron density obtained from a QTAIM analysis is an excellent descriptor of molecular interactions that stabilize and destabilize the formation of the ligand-receptor (L-R) complex. The study was conducted on a series of 25 compounds that have inhibitory effects on DHFR. Besides the synthesis and bioassays performed for some of these compounds, various types of molecular calculations were performed. Thus, we performed MD simulations, computations at different levels of theory (ab initio and DFT) using reduced models and a QTAIM study on the different complexes.The resulting model has allowed us to differentiate not only highly active compounds with respect to compounds weakly active, but also among compounds that have similar affinities in this series. The model also showed a high degree of predictability which allows predicting the affinity of non-synthesized compounds. Very important additional information can be obtained through this type of study, it is possible to visualize which amino acids are involved in the interactions determining the different affinities of the ligands.

Simple model of surface roughness for binary collision sputtering simulations

It has been shown that surface roughness can strongly influence the sputtering yield – especially at glancing incidence angles where the inclusion of surface roughness leads to an increase in sputtering yields. In this work, we propose a simple one-parameter model (the “density gradient model”) which imitates surface roughness effects. In the model, the target’s atomic density is assumed to vary linearly between the actual material density and zero. The layer width is the sole model parameter. The model has been implemented in the binary collision simulator IMSIL and has been evaluated against various geometric surface models for 5keV Ga ions impinging an amorphous Si target. To aid the construction of a realistic rough surface topography, we have performed MD simulations of sequential 5keV Ga impacts on an initially crystalline Si target. We show that our new model effectively reproduces the sputtering yield, with only minor variations in the energy and angular distributions of sputtered particles. The success of the density gradient model is attributed to a reduction of the reflection coefficient – leading to increased sputtering yields, similar in effect to surface roughness.

Experimental and molecular dynamics studies showed that CBP KIX mutation affects the stability of CBP:c-Myb complex

The coactivators CBP (CREBBP) and its paralog p300 (EP300), two conserved multi-domain proteins in eukaryotic organisms, regulate gene expression in part by binding DNA-binding transcription factors. It was previously reported that the CBP/p300 KIX domain mutant (Y650A, A654Q, and Y658A) altered both c-Myb-dependent gene activation and repression, and that mice with these three point mutations had reduced numbers of platelets, B cells, T cells, and red blood cells. Here, our transient transfection assays demonstrated that mouse embryonic fibroblast cells containing the same mutations in the KIX domain and without a wild-type allele of either CBP or p300, showed decreased c-Myb-mediated transcription. Dr. Wright’s group solved a 3-D structure of the mouse CBP:c-Myb complex using NMR. To take advantage of the experimental structure and function data and improved theoretical calculation methods, we performed MD simulations of CBP KIX, CBP KIX with the mutations, and c-Myb, as well as binding energy analysis for both the wild-type and mutant complexes. The binding between CBP and c-Myb is mainly mediated by a shallow hydrophobic groove in the center where the side-chain of Leu302 of c-Myb plays an essential role and two salt bridges at the two ends. We found that the KIX mutations slightly decreased stability of the CBP:c-Myb complex as demonstrated by higher binding energy calculated using either MM/PBSA or MM/GBSA methods. More specifically, the KIX mutations affected the two salt bridges between CBP and c-Myb (CBP-R646 and c-Myb-E306; CBP-E665 and c-Myb-R294). Our studies also revealed differing dynamics of the hydrogen bonds between CBP-R646 and c-Myb-E306 and between CBP-E665 and c-Myb-R294 caused by the CBP KIX mutations. In the wild-type CBP:c-Myb complex, both of the hydrogen bonds stayed relatively stable. In contrast, in the mutant CBP:c-Myb complex, hydrogen bonds between R646 and E306 showed an increasing trend followed by a decreasing trend, and hydrogen bonds of the E665:R294 pair exhibited a fast decreasing trend over time during MD simulations. In addition, our data showed that the KIX mutations attenuate CBP’s hydrophobic interaction with Leu302 of c-Myb. Furthermore, our 500-ns MD simulations showed that CBP KIX with the mutations has a slightly lower potential energy than wild-type CBP. The CBP KIX structures with or without its interacting protein c-Myb are different for both wild-type and mutant CBP KIX, and this is likewise the case for c-Myb with or without CBP, suggesting that the presence of an interacting protein influences the structure of a protein. Taken together, these analyses will improve our understanding of the exact functions of CBP and its interaction with c-Myb.