Effect of electrolyte concentration on DNA A—B conformational transition:An unrestrained molecular dynamics simulation study

The DNA conformational transition depends on both the DNA sequences and environment such as solvent as well as electrolyte in the solution. This paper uses the AMBER8 package to investigate the electrolyte concentration influence on the dynamics of the A→B conformational transition of DNA duplex d（CGCGAATTCGCG）2. The results from the restrained molecular dynamics （MD） simulations indicate that the total energies of the systems for A-DNA are always higher than those for B-DNA, and that the A→B conformational transition in aqueous NaCl solution is a downhill process. The results from the unrestrained MD simulations, as judged by the average distance between the C5＇ atoms （average helical rise per ten base pair）, show that the concentrated NaC1 solution slows down the A→B conformational transition. This observation can be well understood by analyses of the difference between the counterion distributions around A-DNA and B-DNA.

Coarse-Grained Free-Energy Simulations of Conformational State Transitions in an Adenosine 5′-Triphosphate-binding Cassette Exporter

ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics simulations of the potential of mean force along the conformational transition pathway [J. Phys. Chem. B 119, 1295(2015)]. However, the occluded conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this work, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1-d2, which are the COM distances between the two sides of the internal(d1)and the external gate(d2). The potential of mean force is thus obtained to identify the transition pathway, along which several outward-facing, inward-facing, and occluded state structures are predicted in good agreement with structural experiments. Our coarse-grained molecular dynamics free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the inward-facing to outward-facing transition and vice versa during the inward-facing to outward-facing transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the previous result, in which both the internal and external gates are open reported in an X-ray experiment [Proc. Natl. Acad. Sci. USA 104,19005(2007)]. Our study sheds light on the molecular mechanism of the state transitions in an ATP-binding cassette exporter.

Ethylene glycol solution-induced DNA conformational transitions

We study the properties of the ethylene glycol solutions and the conformational transitions of DNA segment in the ethylene glycol solutions by molecular dynamics simulations based on GROMACS. The hydrogen network structures of water–water and ethylene glycol–water are reinforced by ethylene glycol molecules when the concentrations of the solutions increase from 0% to 80%. As illustrated by the results, conformation of the double-stranded DNA in ethylene glycol solutions, although more compact, is similar to the structure of DNA in the aqueous solutions. In contrast, the DNA structure is an A–B hybrid state in the ethanol/water mixed solution. A fraying of terminal base-pairs is observed for the terminal cytosine. The ethylene glycol molecules preferentially form a ring structure around the phosphate groups to influence DNA conformation by hydrogen interactions, while water molecules tend to reside in the grooves. The repulsion between the negatively charged phosphate groups is screened by ethylene glycol molecules, preventing the repulsion from unwinding and extending the helix and thus making the conformation of DNA more compact.

Electric Field-induced Conformational Transition of Bovine Serum Albumin from α-helix to β-sheet

The irreversible conformational transition of bovine serum albumin (BSA) from α-helix to β-sheet, induced by electric field near the electrode surface, was monitored by circular dichroism (CD) with a long optical path thin layer cell (LOPTLC).

LOW ENERGY PATHS AND REORIENTATION OF SIDE-GROUPS OF POLYMERS DURING CONFORMATIONAL STATE TRANSITION

INTRODUCTION The conformational state transition of polymer chains relates to crystallization processes, migration ofthe chains in solution, fluctuation of the end-to-end distance of random coils, and the relaxation and phasetransitions of polymers. A description of the conformational state transition requires questions about; 1) howmany stable conformational states for a specific σ bond; 2) the barriers between the states; 3) the mechanismof the conformational transition; 4) any cooperative behavior during the transition. Flory and his coworkers

Dual-functional poly(2-methyl-2-oxazoline)/poly(2-(dimethylamine)ethyl methacrylate)mixed brushes with switchable protein adsorption and antibacterial properties

Herein,binary mixed brushes consisting of poly(2-methyl-2-oxazoline)(PMOXA)and poly(2-(dimethylamine)ethyl methacrylate)(PDMAEMA)with different chain lengths were fabricated by successive grafting of NH_(2)-terminated PMOXA and SH-terminated PDMAEMA onto polydopamine-anchored substrates.The mixed-brush coating was characterized by variable-angle spectroscopic ellipsometry,X-ray photoelectron spectroscopy,Fourier transform infrared spectroscopy,zeta potential measurements,water contact angle,and atomic force microscopy.The mixed brushes showed tunable surface charge,wettability,and surface roughness,depending on the degree of PDMAEMA swelling under varying pH and ionic strength(Ⅰ).Then the adsorption behaviors of pepsin,bovine serum albumin(BSA),γ-globulin,and lysozyme,four very different proteins with regard to isoelectric point,on the mixed brushes coating were studied by using fluorescence microscopy and surface plasmon resonance.When the chain length of PDMAEMA was about twice as long as PMOXA,the mixed brushes not only had high adsorption capacity for pepsin,BSA,and y-globulin but also had a desorption efficiency of 86.9%,87.1%,and 93.5%,respectively.It is explained that electrostatic attraction between the protonated PDMAEMA and positively charged acidic proteins(pepsin and BSA,whose isoelectric points were below the pK_(a) of PDMAEMA)would drive the intensive adsorption(at pH 3,I=10^(-3)mol·L^(-1)for pepsin,and pH 5,I=10^(-5)mol·L^(-1)for BSA),while desorption was dominated by the hydrophilic PMOXA when PDMAEMA was shrinking(at pH 7,I=10^(-1)mol·L^(-1)for pepsin,and pH 9,I=10^(-1)mol·L^(-1)for BSA).Furthermore,the isoelectric precipitation led to the adsorption of neutral protein(γ-globulin,whose isoelectric point was near the pK_a of PDMAEMA)at pH 7,I=10^(-5)mol·L^(-1),while electrostatic repulsion and antifouling PMOXA triggered the desorption of y-globulin at pH 3,I-10^(-1)mol·L^(-1).However,alkaline protein(lysozyme,whose isoelectric point was higher than the pK_(a) of PDMAEMA)exhibited slight adsorption on PMOXA/PDMAEMA mixed brushes under test conditions,regardless of whether PMOXA or PDMAEMA occupied the outermost layer.The antibacterial property of the mixed brushes against Escherichia coli was investigated.PMOXA/PDMAEMA mixed brushes showed significant bactericidal activity at pH 3,I=10^(-3)mol·L^(-1),while the rinse of pH 9,I=10^(-1)mol·L^(-1)solution could remove most of the residual bacteria.This work not only enables controlled adsorption of proteins with different isoelectric points but also ensures that the surface of the coating is minimized from bacterial contamination.

Piezoelectric fibers based on silk fibroin with excellent output performance

The self-powered tissue engineering scaffold with good biocompatibility is of great significance for stimulating nerve cell growth.In this study,silk fibroin(SF)-based fibers with regulatable structure and piezoelectric performance are fabricated by dry-spinning and post-treatment.The concentration of SF and calcium ion in spinning dope and the post-treatment affect the conformation transition and crystallinity of SF.As a result,the SF fibers exhibit high piezoelectric coefficient d_(33)(3.24 pm/V)and output voltage(~27 V).Furthermore,these piezoelectric fibers promote the growth of PC-12 cells,demonstrating the promising potential for nerve repair and other energy harvester.

The Biochemical Impact by Covalent Shielding of the Anionic Oxygen of the Phosphate Group in DNA and RNA as Methylated Phosphotriester Linkage on the Inhibition of DNA Duplication and on HIV-1 RNA Viral Infectivity Has Been Seriously Overlooked

With the help of model experiments, we are able to offer a detailed proposal for the inhibition of DNA duplication and no inhibition of RNA viral infectivity. As a backbone, we introduced methyl phosphotriester (MPTE). Duplex formation according to the traditional Watson and Crick base-pairing: [(MPTE)n−1 DNA] * DNA and [(MPTE)n−1 DNA] * RNA, where n = number of DNA and RNA bases. However, in the latter case, inhibition is obtained by reduction of the number of MPTE linkages, as is confirmed with model experiments and under biological conditions with micro (mi)RNA substrates. The latter results have recently been published. One or more single MPTEs are disseminated over different places of DNA without neighbour MPTEs (Prof. Wen-Yih Chen and his group, Taiwan).

Visualized thermoresponsive helix-helix switch of polyphenylacetylene with a wide-range tunable transition temperature

Polymers with tunable helicity and naked-eye structural change under external stimuli are valuable for fabricating smart materials. Herein, we report a novel thermoresponsive color and fluorescent polyphenylacetylene switch with a tunable critical temperature. It relies on the temperature and solvent sensitivity of intramolecular n→π* interactions between the vicinal carbonyl groups of ester substituents located at 3,5-positions, which are indispensable for forming the cis-cisoid helical conformation of polyene backbones. In a properly chosen solvent, a compressed cis-cisoid helix is stabilized by n→π* interactions at low temperatures and yields a colorless solution. Increasing temperature causes the conformational transition toward an extended cis-transoid helix due to the disruption of n→π* interactions and produces a yellow solution. Reducing the hydrogen bond donating ability or polarity of solvents increases the switching temperature. By introducing a fluorogenic pendant, this conformational transition can also be read out by fluorescence quenching. This work may open a new window for developing intelligent materials through precisely tuning conformational transitions.

Spectroscopy Investigation on Conformational Transition of Tea Glycoconjugate from Green Tea

The conformational transition of a new glycoconjugate, tea glycoconjugate (TGC), was investigated by spec-troscopy techniques including circular dichroism (CD) and ultraviolet (UV) spectroscopy. The solution behaviors of TGC in the mediums of different temperature, pH value, and ions were compared. Results showed that the native conformation of TGC was partially ordered. The CD value and UV absorbance of TGC altered with the change of pH value, temperature, the addition of ions, and also accompanied order-disorder transition. Especially the condi-tions with temperature higher than the glass transition temperature (Tg=62 ℃), higher pH value or lower pH value will have the most impact on the conformation of TGC, which will destroy the hydrogen bonds between the TGC molecules. The results indicated that the outside factors play important roles on the stability of the conformation of TGC.

Mechanism of Conformational Transition of Silk Fibroin in Alcohol-water Mixtures

Circular dichroism, intrinsic fluorescence of protein and exogenous fluorescence probe of 8-anilino-1-naphtha- lenesulfonic acid hemimagnesium salt （ANS） was used to investigate the mechanism of conformational change of silk fibroin （SF） in aqueous alcohol including methanol and ethanol. The conformational transition of SF from random coil to β-sheet was found to be of a close relationship with the microstructure of the solvent. The alcohol-water mixture at low concentration had little effect on the solvation of the peptide unit, as the inherent water structure was conserved. At high alcohol concentration, the transition from the tetrahedral-like water structure to the chain-like alcohol structure in the mixtures induced a β-sheet conformation of SF, as a result of the formation of intramolecular hydrogen bond between the peptide units in order to eliminate the thermodynamic unfavorite from the contact to the solvent molecules. Meanwhile, the aggregating of hydrophobic side chains was decreased by the alcohol via the destruction of hydrogen bond network of water by alcohol and the binding of alcohol to hydrophobic group.

Protein conformational transitions coupling with ligand interactions:Simulations from molecules to medicine

The functions and activities of proteins are closely related to their structures and dynamics,and their interactions with ligands.Knowledge of the mechanistic events of proteins’conformational transitions and interactions with ligands is crucially important to understand the functions and biological activities of proteins and thus to the design of novel inhibitors of the targeted receptor.In this review article,taking two important systems as examples,i.e.,human immunodeficiency virus type 1 protease(HIV-1 PR)and adenylate kinase(AdK),and focusing on the molecular dynamics simulations of the conformational transitions of protein and the protein-ligand association/dissociation,we explain how the conformational transitions of proteins influence the interactions with their ligands,and how the ligands impact the function and dynamics of proteins.These results of structural dynamics of HIV-1 PR and AdK and their interactions with ligands can help to understand the principle of conformational transitions of proteins,or the interactions of ligands to their biological targets,and thus provide meaningful message in chemistry and biology of drug design and discovery.

Modulation of Conformational Transition of Polypeptides under Slightly Acidic Environment

Controlling the conformational transition of polypeptides under slightly acidic environment is challenging.Herein,we report a class of pH-responsive helix-to-coil conformationally transitionable polypeptides(pCTPs)by simply conjugating tertiary amine groups(TAs)to polylysine.Their conformation is highly dependent on the charge state of TAs,showing a helical structure when most TAs are deprotonated and a non-helical structure when majority of TAs are protonated.The conformational transition pH can be modulated by tuning the hydrophobicity of TAs and the incorporation of hydrophobic monomers at a pH range of 7.2 to 6.0.Such pCTP showed a vesicle-to-micelle transition when their conformation transformed from helix to coil,facilitating controlled drug release.Our study provided an approach to control the conformational transition of polypeptides under slightly acidic condition.

Simulation study on dynamics of A- to B-form transition in aqueous DNA solution:Effect of alkali metal counterions

DNA and its conformational transition can be used to design nanometer-scale structures, nano-tweezers and nanomechanical devices. Experiments and molecular simulations have been used to study the concentration effect on the A-DNA→B-DNA conformational transition, but a systematical investigation on counterion effect on the dynamics of this transition has not been reported up to now. In present work, restrained and unrestrained molecular dynamics （MD） simulations have been performed to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA transitions in aqueous solutions with different alkali metal counterions. The DNA duplex d（CGCGAATTCGCG）2, coion Cl- and counterions Li＋, Na＋, K＋, Rb＋ and Cs~ as well as water molecule were considered using the PARM99 force field in the AMBER8 package. It was found that B-form DNA is more stable than A-form DNA in aqueous electrolyte solutions with different alkali metal counterions. In- creasing KCI concentration in solution hinders the A-DNA^B-DNA transition and the transition times for different alkali metal counterions conform to neither the simple sequence related to naked ion size nor to hydrated diameter, but an apparently abnormal sequence of K＋ 〈 Rb＋ 〈 Cs＋ 〈 Na＋ 〈 Li＋. This abnormal sequence can be well understood in terms of an electrostatic model based on the effective cation diameters and the modified mean-spherical approximation （MMSA）. The present results provide valuable information for the design of DNA-based nanomaterials and nanodevices.

Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution

Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbC1 concentration on the dynamics of the A^B conformational tran- sition in the DNA duplex d（CGCGAATTCGCG）2. Canonical A- and B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was moni- tored for 3.0 ns and the distances between the C5＇ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simula- tions. In addition, increasing the RbC1 concentration in aqueous solution hindered the A^B conformational transition and the transition in aqueous RbC1 solution was faster than that in aqueous NaC1 solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A^B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The ru- bidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help ex- plain the effect of RbC1 concentration on the dynamics of the A^B conformational transition.

Cholesterol modulating the orientation of His17 in hepatitis C virus p7 (5a) viroporin--A molecular dynamic simulation study

Protein p7 of HCV is a 63 amino acid channel forming membrane protein essential for the progression ofviral infection and the sensitivity of this channel to small-molecule inhibitors renders p7 a potentialtarget for novel therapies against HCV infection. Previous biochemical experiments suggested that theHis17 of p7 is a pore-lining residue and solvated-exposed to participate in channel gating. However, arecent NMR structural identification of the p7 hexamer in dodecylphosphocholine （DPC） micellesindicated that the His17 is embedded into the protein matrix. In this work, we performed moleculardynamic simulations to bridge the controversial observations. Our results illustrated that byincorporating the cholesterol into DOPC membranes to mimic an actual membrane-like composition,the orientation of His17 in the hexameric bundles spontaneously access to the central pore region,indicating a versatile property of the p7 viroporin conformation that could be voluntarily influenced byits surrounding environments.