29 research outputs found
UreaāAromatic Stacking and Concerted Urea Transport: Conserved Mechanisms in Urea Transporters Revealed by Molecular Dynamics
Urea
transporters are membrane proteins that selectively allow
urea molecules to pass through. It is not clear how these transporters
allow rapid conduction of urea, a polar molecule, in spite of the
presence of a hydrophobic constriction lined by aromatic rings. The
current study elucidates the mechanism that is responsible for this
rapid conduction by performing free energy calculations on the transporter
dvUT with a cumulative sampling time of about 1.3 Ī¼s. A parallel
arrangement of aromatic rings in the pore enables stacking of urea
with these rings, which, in turn, lowers the energy barrier for urea
transport. Such interaction of the rings with urea is proposed to
be a conserved mechanism across all urea-conducting proteins. The
free energy landscape for the permeation of multiple urea molecules
reveals an interplay between interurea interaction and the solvation
state of the urea molecules. This is for the first time that multiple
molecule permeation through any small molecule transporter has been
modeled
Atomistic Investigation of the Effect of Incremental Modification of Deoxyribose Sugars by Locked Nucleic Acid (Ī²ādāLNA and Ī±ālāLNA) Moieties on the Structures and Thermodynamics of DNAāRNA Hybrid Duplexes
Chemically modified oligonucleotides
offer many possibilities in
utilizing their special features for a vast number of applications
in nucleic acid based therapies and synthetic molecular biology. Locked
nucleic acid analogues (Ī±-/Ī²-LNA) are modifications having
an extra ring of 2ā²-O,4ā²-C-methylene group in the furanose
sugar. LNA strands have been shown to exhibit high binding affinity
toward RNA and DNA strands, and the resultant duplexes show significantly
high melting temperatures. In the present study, molecular dynamics
(MD) simulations were performed on DNAāRNA hybrid duplexes
by systematically modifying their deoxyribose sugars with locked nucleic
acid analogues. Several geometrical and energetic analyses were performed
using principal component (PCA) analysis and binding free energy methods
to understand the consequence of incorporated isomeric LNA modifications
on the structure, dynamics, and stability of DNAāRNA hybrid
duplex. The Ī²-modification systematically changes the conformation
of the DNAāRNA hybrid duplex whereas drastic changes are observed
for Ī±-modification. The fully modified duplexes have distinct
properties compared to partial and unmodified duplexes, and the partly
modified duplexes have properties intermediate to full strand and
unmodified duplexes. The distribution of BI versus BII populations
suggests that backbone rearrangement is minimal for Ī²-LNA modification
in order to accommodate it in duplexes whereas extensive backbone
rearrangement is necessary in order to incorporate Ī±-LNA modification
which subsequently alters the energetic and structural properties
of the duplexes. The simulation results also suggest that the alteration
of DNAāRNA hybrid properties depends on the position of modification
and the gap between the modifications
Structures, Dynamics, and Stabilities of Fully Modified Locked Nucleic Acid (Ī²ādāLNA and Ī±ālāLNA) Duplexes in Comparison to Pure DNA and RNA Duplexes
Locked nucleic acid (LNA) is a chemical
modification which introduces
a āOāCH<sub>2</sub>ā linkage in the furanose
sugar of nucleic acids and blocks its conformation in a particular
state. Two types of modifications, namely, 2ā²-<i>O</i>,4ā²-<i>C</i>-methylene-Ī²-d-ribofuranose
(Ī²-d-LNA) and 2ā²-<i>O</i>,4ā²-<i>C</i>-methylene-Ī±-l-ribofuranose (Ī±-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 Ī±-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. Ļ-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 āOāCH<sub>2</sub>ā linkage in the LNAs vs their absence in the pure duplexes
and similar conformations of the sugar rings in DNA and Ī±-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
Ion Hydration Dynamics in Conjunction with a Hydrophobic Gating Mechanism Regulates Ion Permeation in p7 Viroporin from Hepatitis C Virus
The
selectivity of the p7 channel from hepatitis C virus (HCV)
toward K<sup>+</sup> over Ca<sup>2+</sup> has made the channel an
intriguing system for investigating ion permeation. The present study
employs umbrella sampling free energy calculations to investigate
the atomistic details of cation conduction through the channel. The
free energy profiles suggest that the energy barrier for Ca<sup>2+</sup> conduction is higher than that for K<sup>+</sup> conduction by about
4.5 kcal/mol, thus explaining the selectivity exhibited by the channel
toward K<sup>+</sup>. A hydrophobic stretch in the channel is proposed
to be the primary factor that discriminates K<sup>+</sup> from Ca<sup>2+</sup>, and the ion solvation dynamics in this stretch reveals
interesting insights into the atomistic mechanisms involved. Two-dimensional
free energy landscapes for the ion permeation reveal differences in
the lateral motions of K<sup>+</sup> and Ca<sup>2+</sup> with respect
to the pore axis, and provide additional details of ionāprotein
interactions that govern selectivity
Data_Sheet_1_MO-MEMES: A method for accelerating virtual screening using multi-objective Bayesian optimization.PDF
The pursuit of potential inhibitors for novel targets has become a very important problem especially over the last 2 years with the world in the midst of the COVID-19 pandemic. This entails performing high throughput screening exercises on drug libraries to identify potential āhitsā. These hits are identified using analysis of their physical properties like binding affinity to the target receptor, octanol-water partition coefficient (LogP) and more. However, drug libraries can be extremely large and it is infeasible to calculate and analyze the physical properties for each of those molecules within acceptable time and moreover, each molecule must possess a multitude of properties apart from just the binding affinity. To address this problem, in this study, we propose an extension to the Machine learning framework for Enhanced MolEcular Screening (MEMES) framework for multi-objective Bayesian optimization. This approach is capable of identifying over 90% of the most desirable molecules with respect to all required properties while explicitly calculating the values of each of those properties on only 6% of the entire drug library. This framework would provide an immense boost in identifying potential hits that possess all properties required for a drug molecules.</p
Transannular DielsāAlder Reactivities of 14-Membered Macrocylic Trienes and Their Relationship with the Conformational Preferences of the Reactants: A Combined Quantum Chemical and Molecular Dynamics Study
Transannular DielsāAlder (TADA) reactions that
occur between
the diene and dienophile moieties located on a single macrocyclic triene
molecule have been recognized as effective synthetic routes toward
realizing complex tricyclic molecules in a single step. In this paper,
we report a comprehensive study on the TADA reactions of 14-membered
cyclic triene macrocycles to yield A.B.C[6.6.6] tricycles using quantum
chemical methods and using classical molecular dynamics simulations.
A benchmark study has been performed to examine the reliability of
the commonly used ab initio methods and hybrid density functional
levels of theory in comparison with results from CCSDĀ(T) calculations
to accurately model TADA reactions. The energy barriers obtained using
the M06-2X functional were found to be in quantitative agreement with
the CCSDĀ(T) level of theory using a reasonably large basis set. Conformational
properties of the reactants have been systematically studied using
extensive molecular dynamics (MD) simulations. For this purpose, model
systems were conceived, and force field parameters corresponding to
the dihedral terms in the potential energy function were obtained.
Linear relationship between the activation energies
corresponding to the TADA reactions and the probability of finding
the reactant in certain conformational states was obtained.
A clustering method along with optimizations at the molecular mechanics
and density functional M06-2X levels has been used to locate the most
stable conformation of each of the trienes
Dynamics Based Pharmacophore Models for Screening Potential Inhibitors of Mycobacterial Cyclopropane Synthase
The therapeutic challenges in the
treatment of tuberculosis demand
multidisciplinary approaches for the identification of potential drug
targets as well as fast and accurate techniques to screen huge chemical
libraries. Mycobacterial cyclopropane synthase (CmaA1) has been shown
to be essential for the survival of the bacteria due to its critical
role in the synthesis of mycolic acids. The present study proposes
pharmacophore models based on the structure of CmaA1 taking into account
its various states in the cyclopropanation process, and their dynamic
nature as assessed using molecular dynamics (MD) simulations. The
qualities of these pharmacophore models were validated by mapping
23 molecules that have been previously reported to exhibit inhibitory
activities on CmaA1. Additionally, 1398 compounds that have been shown
to be inactive for tuberculosis were collected from the ChEMBL database
and were screened against the models for validation. The models were
further validated by comparing the results from pharmacophore mapping
with the results obtained from docking these molecules with the respective
protein structures. The best models are suggested by validating all
the models based on their screening abilities and by comparing with
docking results. The models generated from the MD trajectories were
found to perform better than the one generated based on the crystal
structure demonstrating the importance of incorporating receptor flexibility
in drug design
Structural features of the pentamer model.
<p>(A) Kink around the Ile17 residue in the pentamer model. (B) The three residues known to interact with tetherin shown in van der Waals representation.</p
Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch
Riboswitches are structured RNA motifs
that control gene expression
by sensing the concentrations of specific metabolites and make up
a promising new class of antibiotic targets. <i>S</i>-Adenosylmethionine
(SAM)-III riboswitch, mainly found in lactic acid bacteria, is involved
in regulating methionine and SAM biosynthetic pathways. SAM-III riboswitch
regulates the gene expression by switching the translation process
on and off with respect to the absence and presence of the SAM ligand,
respectively. In this study, an attempt is made to understand the
key conformational transitions involved in ligand binding using atomistic
molecular dynamics (MD) simulations performed in an explicit solvent
environment. G26 is found to recognize the SAM ligand by forming hydrogen
bonds, whereas the absence of the ligand leads to opening of the binding
pocket. Consistent with experimental results, the absence of the SAM
ligand weakens the base pairing interactions between the nucleobases
that are part of the Shine-Dalgarno (SD) and anti-Shine-Dalgarno (aSD)
sequences, which in turn facilitates recognition of the SD sequence
by ribosomes. Detailed analysis reveals that a duplex-like structure
formed by nucleotides from different parts of the RNA and the adenine
base of the ligand is crucial for the stability of the completely
folded state in the presence of the ligand. Previous experimental
studies have shown that the SAM-III riboswitch exists in equilibrium
between the unfolded and partially folded states in the absence of
the ligand, which completely folds upon binding of the ligand. Comparison
of the results presented here to the available experimental data indicates
the structures obtained using the MD simulations resemble the partially
folded state. Thus, this study provides a detailed understanding of
the fully and partially folded structures of the SAM-III riboswitch
in the presence and absence of the ligand, respectively. This study
hypothesizes a dual role for the SAM ligand, which facilitates conformational
switching between partially and fully folded states by forming a stable
duplex-like structure and strengthening the interactions between SD
and aSD nucleotides
Molecular Dynamics Simulations Reveal the HIV-1 Vpu Transmembrane Protein to Form Stable Pentamers
<div><p>The human immunodeficiency virus type I (HIV-1) Vpu protein is 81 residues long and has two cytoplasmic and one transmembrane (TM) helical domains. The TM domain oligomerizes to form a monovalent cation selective ion channel and facilitates viral release from host cells. Exactly how many TM domains oligomerize to form the pore is still not understood, with experimental studies indicating the existence of a variety of oligomerization states. In this study, molecular dynamics (MD) simulations were performed to investigate the propensity of the Vpu TM domain to exist in tetrameric, pentameric, and hexameric forms. Starting with an idealized Ī±-helical representation of the TM domain, a thorough search for the possible orientations of the monomer units within each oligomeric form was carried out using replica-exchange MD simulations in an implicit membrane environment. Extensive simulations in a fully hydrated lipid bilayer environment on representative structures obtained from the above approach showed the pentamer to be the most stable oligomeric state, with interhelical van der Waals interactions being critical for stability of the pentamer. Atomic details of the factors responsible for stable pentamer structures are presented. The structural features of the pentamer models are consistent with existing experimental information on the ion channel activity, existence of a kink around the Ile17, and the location of tetherin binding residues. Ser23 is proposed to play an important role in ion channel activity of Vpu and possibly in virus propagation.</p> </div