Conformational Entropy of Biomolecules: Beyond the Quasi-Harmonic Approximation

Numata, Jorge; Wan, Michael; Knapp, Ernst‐Walter

doi:10.1142/9781860949920_0019

Cited by 59 publications

(105 citation statements)

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“…We used ANN program by Mount et al 73 to calculate kth NN entropy and subsequently anharmonic and mutual information estimation following Numata et al 30 and modified it to use in GROMACS 61 analysis program. ' ACKNOWLEDGMENT Author acknowledges Indian Institute of Science Education and Research, Pune for providing the computational facility.…”

Section: ' Computational Detailsmentioning

confidence: 99%

Entropy Balance in the Intercalation Process of an Anti-Cancer Drug Daunomycin

Mukherjee

2011

J. Phys. Chem. Lett.

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I ntercalation 1 is one of the important biophysical processes by which anticancer drugs (such as daunomycin) interact with DNA causing subsequent death of cancerous cells. The enormous therapeutic significance of daunomycin 2 (DM) and related anticancer drugs 3 invoked exhaustive studies on thermodynamic analysis of the intercalation 4À6 and other drugÀDNA binding processes 7,8 portraying a general enthalpy/entropy balance. 9À11 Chaires surmised an interesting aspect of thermodynamic features of drugÀDNA binding from existing experimental observations that intercalation is primarily enthalpy driven, whereas minor groove-binding is entropy driven. 12 For DM intercalation, overall entropy change is small, À1.1 kcal/mol. 12,13 However, identifying molecular contributions to this overall small entropy change is beyond the scope of experiment. The aim of this Letter therefore is to capture entropy contributions of the individual components involved along the intercalation process to probe into the molecular aspects of the thermodynamics of the process, in particular, and recognition processes, in general. This essentially boils down to the calculation of the DM, DNA and water entropy in the different stages along the intercalation process, as adopted in the study providing the first account of such entropy decomposition (including water) in a molecular recognition process.Thermodynamic aspects (enthalpy, entropy) of the overall intercalation process have been studied extensively using experimental techniques 4À6 and computational methods using continuum solvent, 14,15 ab initio quantum calculation, 16 and statistical mechanical approach. 17 However, contributions of various entropic components for intercalation or other molecular recognition processes have not been addressed.Entropy calculation using computational methods is extremely challenging. Only recently, an upsurge of such entropy calculations in various biological systems 18À25 is observed. The most common method to estimate biomolecular entropy is quasi-harmonic (QH) approximation. 26À28 Although it is effective, it suffers from two caveats; it requires long simulations to converge 19 and provides the upper limit of configurational entropy, which often overestimates true entropy. 29 Therefore, various corrections have been proposed 19,30À32 to obtain accurate estimate involving anharmonic and mutual information corrections. Water entropy, however, cannot directly be estimated using QH method because of its diffusive nature. Only recently, Grubmuller and coworkers have proposed a permutation reduction (PR) method to reduce the configurational volume of water by factorial N, thereby allowing the use of QH method for entropy calculation, 33 which has found application in structural changes of DNA and RNA. 18 Another method of calculating water entropy, proposed previously by Goddard and coworkers, 34 has been applied in DNA grooves 35 and bilayer. 36 Entropy change also originates from the loss of rotational and translational degrees of freedom (ΔS t+r ). Ho...

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Section: ' Computational Detailsmentioning

confidence: 99%

Entropy Balance in the Intercalation Process of an Anti-Cancer Drug Daunomycin

Mukherjee

2011

J. Phys. Chem. Lett.

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“…Nevertheless, the calculated binding energies qualitatively reproduced the available experimental order in vitro X-31 human virus strain H3 system [61]. Thus, the large-scale conformational effect with anharmonicity [71][72][73][74][75] did not qualitatively influenced the simple 1:1 binding mode of the selective binding between HA and monovalent sialoside on the basis of fast association rate and fast dissociation rate in equilibrium.…”

Section: The Fragment Molecular Orbital Study Of the Influenza Hemaggmentioning

confidence: 75%

“…The FMO-MP2/PCM study with the molecular mechanics level harmonic normal mode analysis did not consider the full value of the solute entropic change [71][72][73][74][75] via the HAsialoside complex formation. Nevertheless, the calculated binding energies qualitatively reproduced the available experimental order in vitro X-31 human virus strain H3 system [61].…”

Section: The Fragment Molecular Orbital Study Of the Influenza Hemaggmentioning

confidence: 99%

Chemical Insight Into the Influenza A Virus Hemagglutinin Binding to the Sialoside Revealed by the Fragment Molecular Orbital Method

Sawada¹

2012

TOGLYJ

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Abstract:The present mini-review aims first at an introduction to two thermodynamic essentials of the binding between the influenza A virus hemagglutinin (HA) and the cell surface receptor sialoside, (1) the equilibrium 1:1 binding of the HA with the sialoside, (2) the polyvalent effect of the HA binding to the polyvalent sialoside. Second, the review introduces the fragment molecular orbital (FMO) studies of the HA-sialoside (1:1) complexes. The recent FMO method with the polarizable continuum model as one of the residue-based energy analysis method has revealed the role of key amino acid residue on the selective HA subtype H3 binding to the sialosides.

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“…If a simple function such as the Gaussian chosen by Schlitter is used, then the entropies for some modes will be incorrectly estimated; while more complex fitting functions such as the non-parametric histogramming employed in the paper ( Numata et al [2007]) require correspondingly more data to optimise the fit. Although approaches from this "Schlitter family" are certainly useful, their inherent difficulties and limitations suggest that other avenues should also be explored.…”

Section: The Strategy Of Fitting a Distribution To The Partition Funcmentioning

confidence: 99%

Absolute Free Energies for Biomolecules in Implicit or Explicit Solvent

Berryman

Schilling

2014

Physics Procedia

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Methods for absolute free energy calculation by alchemical transformation of a quantitative model to an analytically tractable one are discussed. These absolute free energy methods are placed in the context of other methods, and an attempt is made to describe the best practice for such calculations given the current state of the art. Calculations of the equilibria between the four free energy basins of the dialanine molecule and the two right-and left-twisted basins of DNA are discussed as examples.

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Conformational Entropy of Biomolecules: Beyond the Quasi-Harmonic Approximation

Cited by 59 publications

References 0 publications

Entropy Balance in the Intercalation Process of an Anti-Cancer Drug Daunomycin

Entropy Balance in the Intercalation Process of an Anti-Cancer Drug Daunomycin

Chemical Insight Into the Influenza A Virus Hemagglutinin Binding to the Sialoside Revealed by the Fragment Molecular Orbital Method

Absolute Free Energies for Biomolecules in Implicit or Explicit Solvent

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