Department of Biological Sciences
Permanent URI for this collectionhttp://localhost:4000/handle/123456789/1922
Browse
9 results
Search Results
Item Exploring the Structural Repertoire of Guanine-Rich DNA Sequences: Computer Modelling Studies(Elsiever, 1999) Chowdhury, ShibasishItem Modelling studies on neurodegenerative disease-causing triplet repeat sequences d(GGC/GCC)n and d(CAG/CTG)n(Springer, 2001-12-01) Chowdhury, ShibasishModel 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.Item G-Quadruplex Structure Can Be Stable with Only Some Coordination Sites Being Occupied by Cations: A Six-Nanosecond Molecular Dynamics Study(ACS, 2001) Chowdhury, ShibasishGuanine 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.Item Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide(Wiley, 2002-11-25) Chowdhury, ShibasishThe formation mechanism of an alanine-based peptide has been studied by all-atom molecular dynamics simulations with a recently developed all-atom point-charge force field and the Generalize Born continuum solvent model at an effective salt concentration of 0.2M. Thirty-two simulations were conducted. Each simulation was performed for 100 ns. A surprisingly complex folding process was observed. The development of the helical content can be divided into three phases with time constants of 0.06 – 0.08, 1.4 –2.3, and 12–13 ns, respectively. Helices initiate extreme rapidly in the first phase similar to that estimated from explicit solvent simulations. Hydrophobic collapse also takes place in this phase. A folding intermediate state develops in the second phase and is unfolded to allow the peptide to reach the transition state in the third phase. The folding intermediate states are characterized by the two-turn short helices and the transition states are helix–turn– helix motifs— both of which are stabilized by hydrophobic clusters. The equilibrium helical content, calculated by both the main-chain ⌽–⌿ torsion angles and the main-chain hydrogen bonds, is 64 – 66%, which is in remarkable agreement with experiments. After corrected for the solvent viscosity effect, an extrapolated folding time of 16 –20 ns is obtained that is in qualitative agreement with experiments. Contrary to the prevailing opinion, neither initiation nor growth of the helix is the rate-limiting step. Instead, the rate-limiting step for this peptide is breaking the non-native hydrophobic clusters in order to reach the transition state. The implication to the folding mechanisms of proteins is also discussedItem Ab initio Folding Simulation of the Trp-cage Mini-protein Approaches NMR Resolution(Elsiever, 2003-03-28) Chowdhury, ShibasishHere, we report a 100 ns molecular dynamics simulation of the folding process of a recently designed autonomous-folding mini-protein designated as tc5b with a new AMBER force field parameter set developed based on condensed-phase quantum mechanical calculations and a Generalized Born continuum solvent model. Starting from its fully extended conformation, our simulation has produced a final structure resembling that of NMR native structure to within 1 Å main-chain root mean square deviation. Remarkably, the simulated structure stayed in the native state for most part of the simulation after it reached the state. Of greater significance is that our simulation has not only reached the correct main-chain conformation, but also a very high degree of accuracy in side-chain packing conformation. This feat has traditionally been a challenge for ab initio simulation studies. In addition to characterization of the trajectory, comparison of our results to experimental data is also presented. Analysis of the trajectory suggests that the rate-limiting step of folding of this mini-protein is the packing of the Trp side-chain.Item A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations(Wiley, 2003-09-23) Chowdhury, ShibasishMolecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of ⫽ 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a mooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.Item Fs-21 Peptides Can Form Both Single Helix and Helix−Turn−Helix(ACS, 2004) Chowdhury, ShibasishDetailed folding processes and mechanisms of two alanine-based peptides (Fs-21 and MABA-Fs) were investigated by all atom molecular dynamic simulation with a new AMBER force field and Generalized Born continuum solvent model. Both peptides showed multiphase folding processes. Much like what has been envisaged by the folding funnel theory, the number of accessible conformations descended quickly as folding progresses. Interestingly, MABA-Fs and Fs-21 peptides exhibited notably different folding kinetics; the Fs-21-folding was a two-phase process while MABA-Fs went through three phases and folded more slowly than the Fs-21 peptide by four times. These difference highlights the contribution of the bulky N-terminal MABA group. Furthermore, it is found that helix−turn−helix conformation was the most stable state at 300 K, instead of the expected full helix conformation. At 273 K, however, the full helix became the most stable state. The turn structure was found to be stabilized mainly by the hydrophobic interactions. Statistical analysis of high-resolution PDB structures indicated that most helices are shorter than 16 amino acids. Taken together, we suggest that the intrinsic property of polypeptide chain dictates the formation of short helices in proteins.Item Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations(ACS, 2004) Chowdhury, ShibasishIn this study, the detailed mechanisms of the rapid-folding Trp-cage mini-protein were investigated by extensive all-atom molecular dynamics simulations of both wild-type and mutant proteins using a recently developed point-charge force field within the AMBER simulation package and the generalized Born treatment of solvation. Among the 77 100-ns simulations performed on the wild-type protein, 5 of the simulation trajectories yielded structures with main-chain RMSDs of 1.0−2.0 Å from the native NMR structure. A gradual reduction in the value of the main-chain RMSD distribution was observed during the simulations, which is consistent with the folding funnel theory. The folding time of ∼3 μs based on native tertiary contacts is in reasonable agreement with an experimental value of ∼4 μs. Detailed analysis suggests that packing of the structurally important Trp25 side chain is involved in the rate-limiting step and unfolding of the misfolded states and overcoming the additional entropic barrier also contributed to the rate-limiting steps. This is reinforced by the faster folding rate of the W25F mutant. Two putative folding pathways were observed from the simulations, and their folding rates differed by about 200-fold, leading to a 3.2 kcal/mol folding free energy barrier difference. Of this, approximately 2.2 kcal/mol was due to unfolding of the misfolded states, and about 1.0 kcal/mol was due to overcoming the entropic cost to move Trp25 side chain into the native orientation. Although formation of the main-chain contacts was not the rate-limiting step, we observed a hierarchical process in which the short-range native contacts formed faster than the long-range ones. These observations are consistent with the contact-order theory.Item Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A(ACS, 2005-04) Chowdhury, ShibasishThe folding mechanism of the G29A mutant of the B-domain of protein A (BdpA) has been studied by all-atom molecular dynamics simulation using AMBER force field (ff03) and generalized Born continuum solvent model. Started from the extended chain conformation, a total of 16 simulations (400 ns each) at 300 K captured some early folding events of the G29A mutant of BdpA. In one of the 16 trajectories, the G29A mutant folded within 2.8 Å (root mean square) of the wild-type NMR structure. We observed that the fast burial of hydrophobic residues was the driving force to bring the distant residues into close proximity. The initiation of the helix I and III occurred during the stage of hydrophobic collapse. The initiation and growth of the helix II was slow. Both the secondary structure formation and the development of the native tertiary contacts suggested a multistage folding process. Clustering analysis indicated that two helix species (helices I and III) could be intermediates. Further analysis revealed that the hydrophobic residues of partially folded helix II formed nativelike hydrophobic contacts with helices I and III that stabilized a nativelike state and delayed the completion of folding of the entire protein. The details of the early folding process were compared with other theoretical and experimental studies. It was found that a nativelike hydrophobic cluster was formed by residues including F30, I31, L34, L44, L45, and A48 that prevented further development of the native structures, and breaking the hydrophobic cluster like this one contributed to the rate-limiting step. This was in complete agreement with the recent kinetic measurements in which mutations of these residues to Gly and Ala substantially increased the folding rates by as much as 60 times. Apparently, destabilization of nonnative states dramatically enhanced the folding rates.