Abstract

Locked nucleic acid (LNA) is a chemical modification which introduces a -O-CH2-linkage in the furanose sugar of nucleic acids and blocks its conformation in a particular state. Two types of modifications, namely, 2'-O,4'-C-methylene-β-D-ribofuranose (β-D-LNA) and 2'-O,4'-C-methylene-α-L-ribofuranose (α-L-LNA), have been shown to yield RNA and DNA duplex-like structures, respectively. LNA modifications lead to increased melting temperatures of DNA and RNA duplexes, and have been suggested as potential therapeutic agents in antisense therapy. In this study, molecular dynamics (MD) simulations were performed on fully modified LNA duplexes and pure DNA and RNA duplexes sharing a similar sequence to investigate their structure, stabilities, and solvation properties. Both LNA duplexes undergo unwinding of the helical structure compared to the pure DNA and RNA duplexes. Though the α-LNA substituent has been proposed to mimic deoxyribose sugar in its conformational properties, the fully modified duplex was found to exhibit unique structural and dynamic properties with respect to the other three nucleic acid structures. Free energy calculations accurately capture the enhanced stabilization of the LNA duplex structures compared to DNA and RNA molecules as observed in experiments. π-stacking interaction between bases from complementary strands is shown to be one of the contributors to enhanced stabilization upon LNA substitution. A combination of two factors, namely, nature of the -O-CH2- linkage in the LNAs vs their absence in the pure duplexes and similar conformations of the sugar rings in DNA and α-LNA vs the other two, is suggested to contribute to the stark differences among the four duplexes studied here in terms of their structural, dynamic, and energetic properties

Abstract

The emergence of single-molecule force measurement experiments has facilitated a better understanding of protein folding pathways and the thermodynamics involved. Computational methods such as steered molecular dynamics (SMD) simulations are helpful in providing atomistic level information on the unfolding pathways. Recent experimental studies have showed that combinations of single-molecule experiments with traditional methods such as chemical and/or thermal denaturation yield additional insights into the folding phenomenon. In this study, we report results from extensive computations (a total of about 60 SMD simulations with a total length of about 0.4 μs) that address the effect of thermal perturbation on the mechanical stability of the I27 domain of the protein titin. A wide range of temperatures (280–340 K) were considered for the pulling, which was done at both constant velocity and constant force using SMD simulations. Good agreement with experimental data, such as for the trends in changes in average force and the maximum force with respect to the temperature, was obtained. This study identifies two competing pathways for the mechanical unfolding of I27, and illustrates the significance of combining various techniques to examine protein foldin

Abstract

The role of salt bridges in chromatin protein Sso7d, from S. solfataricus has previously been shown to be crucial for its unusual high thermal stability. Experimental studies have shown that single site mutation of Sso7d (F31A) leads to a substantial decrease in the thermal stability of this protein due to distortion of the hydrophobic core. In the present study, we have performed a total of 0.2s long molecular dynamics (MD) simulations on F31A at room temperature, and at 360 K, close to the melting temperature of the wild type (WT) protein to investigate the role of hydrophobic core on protein stability. Sso7d-WT was shown to be stable at both 300 and 360 K; however, F31A undergoes denaturation at 360 K, consistent with experimental results. The structural and energetic properties obtained using the analysis of MD trajectories indicate that the single mutation results in high flexibility of the protein, and loosening of intramolecular interactions. Correlation between the dynamics of the salt bridges with the structural transitions and the unfolding pathway indicate the importance of both salt bridges and hydrophobic in effecting thermal stability of proteins in general.

Abstract

A series of dihydrogen complexes trans-[Ru(η2-H2){SC(SR)H}(dppe)2][X][BF4] (R = CH3, X = OTf; R = C6H5CH2, X = BPh4; R = H2C=CHCH2, X = BPh4; dppe = Ph2PCH2CH2PPh2) bearing sulfur-donor ligands has been synthesized by protonation of the (alkyl dithioformate)hydrido complexes trans-[Ru(H){SC(SR)H}(dppe)2][X] by using HBF4•Et2O. Competitive substitution reactions between H2 and SC(SR)H in trans-[Ru(η2-H2){SC(SR)H}(dppe)2][X][BF4] have been studied by treatment with CH3CN, CO, and P(OCH3)3. These resulted in the expulsion of SC(SR)H from the metal center, thus indicating that the alkyl dithioformate ligand is more labile than H2. Bonding of alkyl dithioformate ligands (sulfur-donor ligands) trans to H2 have been studied by comparing the H–H distances and chemical-shift values (1H NMR spectroscopy) of the various dihydrogen complexes bearing different trans ligands. This study qualitatively suggests that the alkyl dithioformate ligands in these trans-dihydrogen complexes show a poor π effect, and it is further supported by density functional theory calculations. The first example of a dihydrogen complex bearing dithioformic acid, trans-[Ru(η2-H2){SC(SH)H}(dppe)2][BF4]2, was obtained by protonation of trans-[Ru(H){SC(S)H}(dppe)2] by using HBF4•Et2O.

Abstract

In the late 19th century, van’t Hoff and Le Bel proposed that carbon prefers a tetrahedral arrangement in its tetracoordinate form. Similarly, the isoelectronic species such as B-, N+, Al-, Si and P+ assume tetrahedral arrangement. However, it has been shown by several research groups that planar arrangement for tetracoordinated carbon centers may be possible for certain molecules that are stabilized by steric constraints and electronic effects. Sastry and coworkers have identified a series of neutral hydrocarbons that are stable in their planar form. We have done high level quantum chemical calculations on skeletally substituted derivative of one of the hydrocarbons (C5H4). Interestingly, the phosphonium ion (C4PH4 +) is found to be a minimum on its potential energy surface consistently by both density functional theory and MP2 methods. A transition state corresponding to the interconversion between the two forms was identified, which indicates rapid transitions. Additionally, the tetrahedral form was found to be the minima for C and B-. The tetrahedral form is the minima for Al- and Si, whereas the planar form was characterized as a transition state that connects two identical tetrahedral forms. Ab initio molecular dynamics calculations indicate that C4H4Si does undergo rapid interconversion between two identical tetrahedral structures through the planar transition state in the femtosecond timescale. However, C4H4P+ and C4H4Al- undergoes irreversible ring opening during the simulations. These molecules/ions were further analyzed using NICS calculations and ring opening reactivities.

Abstract

Due to poor stability and nature of low nuclease resistance of pure nucleic acids, a suitable chemical modification is required which improves several factors such as increased cellular uptake, altered duplex conformation and stability. In general, the modifications at ribose sugar (backbone) of the oligonucleotide attribute special features to the duplexes than other modifications. Some of the common modifications include 2'-O-methyl, 2'-O,4'-C-methylene-β-D-ribofuranosyl (LNA) and phosphoroamidate. The modified oligonucleotides have also been shown to be potential antisense agents. Molecular dynamics (MD) simulations are valuable tools to study nucleic acid dynamics, conformational preferences, stabilities etc. Here, we have employed different simulation techniques such as traditional MD, replica exchange MD to understand the properties of modified duplexes and also the origin for the effect of chemical modification. The simulations revealed several important aspects related to duplex stability and relation with their base content. The factors responsible for the stability/unstability of modified duplexes with different sequences are also examined. Our results also suggest that the differential changes observed in nucleic acids depends on the position, nature of the modified site. This study also provides a molecular level picture of structural changes arising due to different types of modifications which is important in designing antisense oligonucleotides.

Abstract

The structure and ion channel activity of the viral ion channels Vpu from human immunodeficiency virus type I (HIV-1) and 3a from SARS Coronavirus (SARS-CoV) have not been characterised in atomistic detail, in spite of the physiological importance of these ion channels. We have modelled several possible oligomeric states for Vpu, and carried out extensive molecular dynamics (MD) simulations in a lipid bilayer environment. Our results show that the pentamer is the most stable oligomeric form, with van der Waals interactions being the dominant force in holding together the monomeric units. The mechanism of ion conduction through the pentameric form has been investigated by umbrella sampling free energy calculations. We suggest that only one ion can pass through the channel at a time, rather than a continuous stream of ions; this is in agreement with experimental conductance studies [1]. We have also modelled possible structures for a monomeric unit of the ion channel SARS 3a, which has three helical transmembrane (TM) domains connected by loops [2]. Based on residue orientation, clusters of hydrophilic residues have been identified in each TM domain, and, by considering all possible orientations of these hydrophilic clusters, a number of monomers have been modelled and equilibrated in a membrane environment. We shall be presenting model structures of both monomeric and oligomeric states of 3a

Abstract

: Density functional B3LYP method was used to investigate the preference of intra and intermolecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.

Abstract

t has been proposed that combining chemical and thermal denaturation along with mechanical unfolding enables better understanding of the thermodynamics of protein folding, and associated pathways. We have used molecular dynamics (MD) simulations, and umbrella sampling technique to study the effect of thermal and chemical perturbations on the unfolding of Trp-cage miniprotein (TC5b). Free energy profiles for the unfolding of the minicage protein were obtained at two different temperatures, and in presence and absence of urea. The distance between the penultimate terminal residues was used as the reaction coordinate for calculating the free energies. The unfolding involves opening of the Trp-cage, and separation of the secondary structure elements followed by the unfolding of the α-helix. Several energetic and geometric analyses including inter- and intramolecular interactions, and radial distribution functions and their relevance to the folding pathways will be discussed. Similar study on the titin I27 protein will also be presented.

Abstract

SAM-III riboswitch present in the 5’-UTR of mRNA that translates to SAM synthetase in certain bacteria is involved in regulating the biosynthesis of S-adenosylmethionine (SAM) by acting as an on-off switch for the translation process. We have used molecular dynamics (MD) and steered MD simulations to understand the ligand recognition and the switching mechanisms. Computations on model systems indicated that the riboswitch does not recognize SAM over a structurally related analog, S-adenosylhomocysteine (SAH). Nonetheless, the RNA uses nonspecific interactions to stabilize SAM in its binding pocket compared to SAH. Calculations were done in the absence of the ligand to examine the conformational changes responsible for the transition between on and off states. While the on- state is capable of sampling a large conformational space, formation of duplexlike structure comprising the adenine part of the ligand and sequentially distant nucleotides seems to be crucial for the on- to off- state transition.