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Themed collection Theoretical chemical physics of biological systems

23 items
Perspective

Computational enzymatic catalysis – clarifying enzymatic mechanisms with the help of computers

Computational methods offer an unparalleled opportunity to dissect in minute detail enzymatic reaction mechanisms.

Graphical abstract: Computational enzymatic catalysis – clarifying enzymatic mechanisms with the help of computers
Perspective

Implementation and validation of a multi-purpose virtual spectrometer for large systems in complex environments

Toward a multifrequency virtual spectrometer: status and perspectives.

Graphical abstract: Implementation and validation of a multi-purpose virtual spectrometer for large systems in complex environments
Perspective

On developing coarse-grained models for biomolecular simulation: a review

A review of the basic ingredients of developing coarse-grained models and conditions to be satisfied for preserving the correct physical mechanisms.

Graphical abstract: On developing coarse-grained models for biomolecular simulation: a review
Paper

Identifying the sarco(endo)plasmic reticulum Ca2+ ATPase (SERCA) as a potential target for hypericin – a theoretical study

The chemical structure of hypericin and the crystal structure of SERCA1A with the identified binding pockets that were subject to docking in the present study.

Graphical abstract: Identifying the sarco(endo)plasmic reticulum Ca2+ ATPase (SERCA) as a potential target for hypericin – a theoretical study
Paper

A first step towards the understanding of the 5-HT3 receptor subunit heterogeneity from a computational point of view

The physicochemical characterization of the several 5-HT3-R interfaces allows the prediction, on atomistic bases, of the role played by the extracellular moieties of the A–E subunits in the formation of functional or non-functional receptors.

Graphical abstract: A first step towards the understanding of the 5-HT3 receptor subunit heterogeneity from a computational point of view
Paper

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

We show severe convergence problems for QM/MM free-energy perturbations even if based on tailored force fields or semiempirical calculations.

Graphical abstract: Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations
Paper

Theoretical studies of HIV-1 reverse transcriptase inhibition

Computational methods for accurately calculating the binding affinity of a ligand for a protein play a pivotal role in rational drug design.

Graphical abstract: Theoretical studies of HIV-1 reverse transcriptase inhibition
Paper

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

Towards elucidating the role of base stacking in the conformational preference of tandem GA base pairs in RNA.

Graphical abstract: Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes
Paper

The catalytic mechanism of mouse renin studied with QM/MM calculations

The picture shows the enzyme renin, whose catalytic mechanism was studied in atomistic detail. The enzyme is coloured grey, the substrate is coloured orange, and the cleavage point (Leu10-Val11), the catalytic aspartic dyad and the water molecule are coloured by element, and depicted in ball and stick representation.

Graphical abstract: The catalytic mechanism of mouse renin studied with QM/MM calculations
Paper

Quantum chemical modeling of rhodopsin mutants displaying switchable colors

The color variation of computationally designed rhodopsin mutants is investigated using a multiconfigurational quantum chemistry based QM/MM method.

Graphical abstract: Quantum chemical modeling of rhodopsin mutants displaying switchable colors
Paper

Interaction of C70 fullerene with the Kv1.2 potassium channel

Voltage-gated potassium channels exposed to fullerene.

Graphical abstract: Interaction of C70 fullerene with the Kv1.2 potassium channel
Paper

Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

MD simulations of E2 enzymes were carried out and analyzed to provide a quantitative description of their functional dynamics. The functionally relevant differences between the closed and open conformations were unravelled, and critical residues involved in long-range communication paths were detected.

Graphical abstract: Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation
Paper

A hybrid elastic band string algorithm for studies of enzymatic reactions

In this work we describe a computationally efficient algorithm to determine minimum energy paths in complex systems.

Graphical abstract: A hybrid elastic band string algorithm for studies of enzymatic reactions
Paper

Stability and iron coordination in DNA adducts of Anthracycline based anti-cancer drugs

There is evidence that the interaction of the α-ketol group of the Doxorubicin and Epirubicin anti-cancer drugs with Fe(III) generates hydroxyl radicals under aerobic conditions, which may cause cardiotoxicity in patients.

Graphical abstract: Stability and iron coordination in DNA adducts of Anthracycline based anti-cancer drugs
Paper

Reactions of cisplatin and glycine in solution with constant pH: a computational study

In this study interaction between glycine and cisplatin is explored.

Graphical abstract: Reactions of cisplatin and glycine in solution with constant pH: a computational study
Paper

Spectral properties of polypyridyl ruthenium complexes intercalated in DNA: theoretical insights into the surrounding effects of [Ru(dppz)(bpy)2]2+

The UV/Visible absorption properties of a polypyridyl ruthenium complex upon intercalation on DNA are studied at the mixed quantum mechanics molecular mechanics level of theory.

Graphical abstract: Spectral properties of polypyridyl ruthenium complexes intercalated in DNA: theoretical insights into the surrounding effects of [Ru(dppz)(bpy)2]2+
Paper

On the evolution of one-electron-oxidized deoxyguanosine in damaged DNA under physiological conditions: a DFT and ONIOM study on proton transfer and equilibrium

Deprotonation of ground-state deoxyguanosine sites in one-electron-oxidized DNA has been investigated, including both the purine and the sugar moieties. A new mechanistic proposal is provided supporting the formation of C centered radicals under physiological conditions.

Graphical abstract: On the evolution of one-electron-oxidized deoxyguanosine in damaged DNA under physiological conditions: a DFT and ONIOM study on proton transfer and equilibrium
Paper

XYG3 and XYGJ-OS performances for noncovalent binding energies relevant to biomolecular structures

XYG3 and XYGJ-OS functionals provide an overall good agreement with reference values for the S22, S22x5 and JSCH-2005 benchmark sets.

Graphical abstract: XYG3 and XYGJ-OS performances for noncovalent binding energies relevant to biomolecular structures
Paper

Aluminum speciation in biological environments. The deprotonation of free and aluminum bound citrate in aqueous solution

Investigation on the structure and acidity of citric acid upon its complexation to Al(III).

Graphical abstract: Aluminum speciation in biological environments. The deprotonation of free and aluminum bound citrate in aqueous solution
Paper

On the peroxyl scavenging activity of hydroxycinnamic acid derivatives: mechanisms, kinetics, and importance of the acid–base equilibrium

Excellent antioxidants in aqueous solution, at physiological pH, via a single electron transfer mechanism from the phenoxide anions.

Graphical abstract: On the peroxyl scavenging activity of hydroxycinnamic acid derivatives: mechanisms, kinetics, and importance of the acid–base equilibrium
Paper

Cisplatin cytotoxicity: a theoretical study of induced mutations

This multi-scale theoretical study provides new insights into the cisplatin biological activity. The induced rare tautomeric form of the guanine–cytosine base pair in the A[G with combining low line][G with combining low line] context emerges as a well-suited candidate to promote its in vivo cytotoxicity.

Graphical abstract: Cisplatin cytotoxicity: a theoretical study of induced mutations
Paper

Turn-directed folding dynamics of β-hairpin-forming de novo decapeptide Chignolin

Extensive, unbiased simulations of a 10-residue β-hairpin disclose a turn-directed folding process and show that hydrophobic cross-strand side-chain interactions may cause packing frustration that could nucleate aggregative events.

Graphical abstract: Turn-directed folding dynamics of β-hairpin-forming de novo decapeptide Chignolin
Paper

Why voltage-gated Ca2+ and bacterial Na+ channels with the same EEEE motif in their selectivity filters confer opposite metal selectivity

We provide a physical basis for the opposite ion selectivity in Nav and Cav channels with the EEEE motif.

Graphical abstract: Why voltage-gated Ca2+ and bacterial Na+ channels with the same EEEE motif in their selectivity filters confer opposite metal selectivity
23 items

About this collection

PCCP is delighted to present a themed issue on  theoretical chemical physics of biological systems,  Guest Edited by Carlo Adamo, Leif Eriksson, Maria João Ramos, Nino Russo and Jesus Ugalde.

Theoretical chemical physics of biological systems has as its main aim the qualitative (and often quantitative) understanding of biological and biomolecular systems on different time and size scale, from angstrom to centimetres, from femtoseconds to hours.  By its very nature theoretical chemical physics of biological systems is wonderfully diverse, and applications range over a vast number of topics.

This themed issue covers the most recent developments in the field of modeling and simulation of biological systems, new methodology and applications on "hot" topics such as drug modeling and development, enzymatic mechanisms, protein interactions, and much more.

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