Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex

AbstractBase pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti & + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery.

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Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

10.26434/chemrxiv.7376081 ◽

2019 ◽

Author(s):

Xiaohui Wang ◽

Zhaoxi Sun

Keyword(s):

Free Energy ◽

Energy Landscape ◽

Sampling Technique ◽

Umbrella Sampling ◽

Energy Simulation ◽

Nonlinear Dependence ◽

Free Energy Landscape ◽

Convergence Criterion ◽

Base Flipping ◽

Convergence Behavior

Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size.

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Effect of Ionic Strength on the Aggregation Propensity of Aβ1-42 Peptide: An In-silico Study

Current Chemical Biology ◽

10.2174/2212796814999200818103157 ◽

2020 ◽

Vol 14 (3) ◽

pp. 216-226

Author(s):

Priyanka Borah ◽

Venkata S.K. Mattaparthi

Keyword(s):

Diffusion Coefficient ◽

Ionic Strength ◽

Marked Effect ◽

Computational Study ◽

Conformational Dynamics ◽

Rapid Change ◽

Md Simulations ◽

Radius Of Gyration ◽

Aggregation Propensity ◽

In Silico Study

Background: Aggregation of misfolded proteins under stress conditions in the cell might lead to several neurodegenerative disorders. Amyloid-beta (Aβ1-42) peptide, the causative agent of Alzheimer’s disease, has the propensity to fold into β-sheets under stress, forming aggregated amyloid plaques. This is influenced by factors such as pH, temperature, metal ions, mutation of residues, and ionic strength of the solution. There are several studies that have highlighted the importance of ionic strength in affecting the folding and aggregation propensity of Aβ1-42 peptide. Objective: To understand the effect of ionic strength of the solution on the aggregation propensity of Aβ1-42 peptide, using computational approaches. Materials and Methods: In this study, Molecular Dynamics (MD) simulations were performed on Aβ1-42 peptide monomer placed in (i) 0 M, (ii) 0.15 M, and (iii) 0.30 M concentration of NaCl solution. To prepare the input files for the MD simulations, we have used the Amberff99SB force field. The conformational dynamics of Aβ1-42 peptide monomer in different ionic strengths of the solutions were illustrated from the analysis of the corresponding MD trajectory using the CPPtraj tool. Results: From the MD trajectory analysis, we observe that with an increase in the ionic strength of the solution, Aβ1-42 peptide monomer shows a lesser tendency to undergo aggregation. From RMSD and SASA analysis, we noticed that Aβ1-42 peptide monomer undergoes a rapid change in conformation with an increase in the ionic strength of the solution. In addition, from the radius of gyration (Rg) analysis, we observed Aβ1-42 peptide monomer to be more compact at moderate ionic strength of the solution. Aβ1-42 peptide was also found to hold its helical secondary structure at moderate and higher ionic strengths of the solution. The diffusion coefficient of Aβ1-42 peptide monomer was also found to vary with the ionic strength of the solution. We observed a relatively higher diffusion coefficient value for Aβ1-42 peptide at moderate ionic strength of the solution. Conclusion: Our findings from this computational study highlight the marked effect of ionic strength of the solution on the conformational dynamics and aggregation propensity of Aβ1-42 peptide monomer.

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Correlation of membrane protein conformational and functional dynamics

Nature Communications ◽

10.1038/s41467-021-24660-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Raghavendar Reddy Sanganna Gari ◽

Joel José Montalvo‐Acosta ◽

George R. Heath ◽

Yining Jiang ◽

Xiaolong Gao ◽

...

Keyword(s):

Membrane Protein ◽

Conformational Changes ◽

Single Channel ◽

Conformational Dynamics ◽

Md Simulations ◽

High Temporal Resolution ◽

Dependent Manner ◽

Functional Dynamics ◽

Ph Dependent ◽

Open States

AbstractConformational changes in ion channels lead to gating of an ion-conductive pore. Ion flux has been measured with high temporal resolution by single-channel electrophysiology for decades. However, correlation between functional and conformational dynamics remained difficult, lacking experimental techniques to monitor sub-millisecond conformational changes. Here, we use the outer membrane protein G (OmpG) as a model system where loop-6 opens and closes the β-barrel pore like a lid in a pH-dependent manner. Functionally, single-channel electrophysiology shows that while closed states are favored at acidic pH and open states are favored at physiological pH, both states coexist and rapidly interchange in all conditions. Using HS-AFM height spectroscopy (HS-AFM-HS), we monitor sub-millisecond loop-6 conformational dynamics, and compare them to the functional dynamics from single-channel recordings, while MD simulations provide atomistic details and energy landscapes of the pH-dependent loop-6 fluctuations. HS-AFM-HS offers new opportunities to analyze conformational dynamics at timescales of domain and loop fluctuations.

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Tethering-induced destabilization and ATP-binding for tandem RRM domains of ALS-causing TDP-43 and hnRNPA1

Scientific Reports ◽

10.1038/s41598-020-80524-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mei Dang ◽

Yifan Li ◽

Jianxing Song

Keyword(s):

Conformational Dynamics ◽

Md Simulations ◽

Atp Binding ◽

Rna Recognition Motif ◽

Rna Recognition ◽

Nucleic Acid Binding ◽

General Role ◽

Nmr Characterization ◽

Lateral Sclerosis

AbstractTDP-43 and hnRNPA1 contain tandemly-tethered RNA-recognition-motif (RRM) domains, which not only functionally bind an array of nucleic acids, but also participate in aggregation/fibrillation, a pathological hallmark of various human diseases including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), alzheimer's disease (AD) and Multisystem proteinopathy (MSP). Here, by DSF, NMR and MD simulations we systematically characterized stability, ATP-binding and conformational dynamics of TDP-43 and hnRNPA1 RRM domains in both tethered and isolated forms. The results reveal three key findings: (1) upon tethering TDP-43 RRM domains become dramatically coupled and destabilized with Tm reduced to only 49 °C. (2) ATP specifically binds TDP-43 and hnRNPA1 RRM domains, in which ATP occupies the similar pockets within the conserved nucleic-acid-binding surfaces, with the affinity slightly higher to the tethered than isolated forms. (3) MD simulations indicate that the tethered RRM domains of TDP-43 and hnRNPA1 have higher conformational dynamics than the isolated forms. Two RRM domains become coupled as shown by NMR characterization and analysis of inter-domain correlation motions. The study explains the long-standing puzzle that the tethered TDP-43 RRM1–RRM2 is particularly prone to aggregation/fibrillation, and underscores the general role of ATP in inhibiting aggregation/fibrillation of RRM-containing proteins. The results also rationalize the observation that the risk of aggregation-causing diseases increases with aging.

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Structural insights into the repair mechanism of AGT for methyl-induced DNA damage

Biological Chemistry ◽

10.1515/hsz-2021-0198 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Rajendra P. Koirala ◽

Rudramani Pokhrel ◽

Prabin Baral ◽

Purushottam B. Tiwari ◽

Prem P. Chapagain ◽

...

Keyword(s):

Covalent Bond ◽

Cancer Therapeutics ◽

Md Simulations ◽

Structural Features ◽

Umbrella Sampling ◽

Repair Mechanism ◽

Structural Investigations ◽

Methylated Dna ◽

Dna Base ◽

Dna Alkyltransferase

Abstract Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and for the protein-DNA covalent bond will allow investigations of the DNA repair mechanism as well as the exploration of cancer therapeutics targeting the AGT-DNA complexes at various functional states as well as explorations via stabilization of the complex.

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A molecular journey to check the conformational dynamics of tau tubulin kinase 2 mutations associated with Alzheimer's disease

RSC Advances ◽

10.1039/d0ra07659g ◽

2021 ◽

Vol 11 (3) ◽

pp. 1320-1331

Author(s):

Shahzaib Ahamad ◽

Hema Kanipakam ◽

Vijay Kumar ◽

Dinesh Gupta

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Conformational Dynamics ◽

Md Simulations

MD simulations of TTBK2 mutants to study its impact on stability of the protein.

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Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs

10.1101/2021.06.28.450193 ◽

2021 ◽

Author(s):

Zachary Smith ◽

Pratyush Tiwary

Keyword(s):

Belief Propagation ◽

Conformational Dynamics ◽

Joint Probability ◽

Md Simulations ◽

Distribution Functions ◽

Factor Graph ◽

High Dimensional ◽

Enhanced Sampling ◽

Small Peptides ◽

Approximate Probability

Molecular dynamics (MD) simulations provide a wealth of high-dimensional data at all-atom and femtosecond resolution but deciphering mechanistic information from this data is an ongoing challenge in physical chemistry and biophysics. Theoretically speaking, joint probabilities of the equilibrium distribution contain all thermodynamic information, but they prove increasingly difficult to compute and interpret as the dimensionality increases. Here, inspired by tools in probabilistic graphical modeling, we develop a factor graph trained through belief propagation that helps factorize the joint probability into an approximate tractable form that can be easily visualized and used. We validate the study through the analysis of the conformational dynamics of two small peptides with 5 and 9 residues. Our validations include testing the conditional dependency predictions through an intervention scheme inspired by Judea Pearl. Secondly we directly use the belief propagation based approximate probability distribution as a high-dimensional static bias for enhanced sampling, where we achieve spontaneous back-and-forth motion between metastable states that is up to 350 times faster than unbiased MD. We believe this work opens up useful ways to thinking about and dealing with high-dimensional molecular simulations.

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Molecular simulations of lipid membrane partitioning and translocation by bacterial quorum sensing modulators

PLoS ONE ◽

10.1371/journal.pone.0246187 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0246187

Author(s):

Tianyi Jin ◽

Samarthaben J. Patel ◽

Reid C. Van Lehn

Keyword(s):

Quorum Sensing ◽

Lipid Bilayers ◽

Lipid Membrane ◽

Computational Cost ◽

Md Simulations ◽

Umbrella Sampling ◽

Communication Process ◽

Free Energies ◽

Membrane Partitioning ◽

Solvent Model

Quorum sensing (QS) is a bacterial communication process mediated by both native and non-native small-molecule quorum sensing modulators (QSMs), many of which have been synthesized to disrupt QS pathways. While structure-activity relationships have been developed to relate QSM structure to the activation or inhibition of QS receptors, less is known about the transport mechanisms that enable QSMs to cross the lipid membrane and access intracellular receptors. In this study, we used atomistic MD simulations and an implicit solvent model, called COSMOmic, to analyze the partitioning and translocation of QSMs across lipid bilayers. We performed umbrella sampling at atomistic resolution to calculate partitioning and translocation free energies for a set of naturally occurring QSMs, then used COSMOmic to screen the water-membrane partition and translocation free energies for 50 native and non-native QSMs that target LasR, one of the LuxR family of quorum-sensing receptors. This screening procedure revealed the influence of systematic changes to head and tail group structures on membrane partitioning and translocation free energies at a significantly reduced computational cost compared to atomistic MD simulations. Comparisons with previously determined QSM activities suggest that QSMs that are least likely to partition into the bilayer are also less active. This work thus demonstrates the ability of the computational protocol to interrogate QSM-bilayer interactions which may help guide the design of new QSMs with engineered membrane interactions.

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Exploration of inositol 1,4,5-trisphosphate (IP3) regulated dynamics of N-terminal domain of IP3 receptor reveals early phase molecular events during receptor activation

10.1101/404020 ◽

2018 ◽

Author(s):

Aneesh Chandran ◽

Xavier Chee ◽

David L. Prole ◽

Taufiq Rahman

Keyword(s):

Conformational Dynamics ◽

Md Simulations ◽

Receptor Activation ◽

Activation Mechanism ◽

Ip3 Receptor ◽

Dynamic Correlation ◽

Molecular Events ◽

Binding Core ◽

Domain Dynamics ◽

Phosphate Groups

Inositol 1, 4, 5-trisphosphate (IP3) binding at the N-terminus (NT) of IP3 receptor (IP3R) allosterically triggers the opening of a Ca2+-conducting pore located ~ 100 Å away from the IP3-binding core (IBC). However, the precise mechanism of IP3 binding and correlated domain dynamics in the NT that are central to the IP3R activation, remains unknown. Our all-atom molecular dynamics (MD) simulations recapitulate the characteristic twist motion of the suppresser domain (SD) and reveal correlated ‘clam closure’ dynamics of IBC with IP3-binding, complementing existing suggestions on IP3R activation mechanism. Our study further reveals the existence of inter-domain dynamic correlation in the NT and establishes the SD to be critical for the conformational dynamics of IBC. Also, a tripartite interaction involving Glu283-Arg54-Asp444 at the SD – IBC interface seemed critical for IP3R activation. Intriguingly, during the sub-microsecond long simulation, we observed Arg269 undergoing an SD-dependent flipping of hydrogen bonding between the first and fifth phosphate groups of IP3. This seems to play a major role in determining the IP3 binding affinity of IBC in the presence/absence of the SD. Our study thus provides atomistic details of early molecular events occurring within the NT during and following IP3 binding that lead to channel gating.

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Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics

10.26434/chemrxiv.5469241.v1 ◽

2017 ◽

Author(s):

Irfan Alibay ◽

Kepa K. Burusco ◽

Neil J. Bruce ◽

Richard A. Bryce

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Md Simulations ◽

Umbrella Sampling ◽

Biological Action ◽

Sialyl Lewis X ◽

Enhanced Sampling ◽

Sialyl Lewis ◽

Aqueous Solvent ◽

A Minor

Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 ms trajectories; these simulations find a predominance of closed conformer and a range of low occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4C1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution, corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 ms unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.

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