The VES Hypothesis and Protein Conformational Changes
Abstract
This work started as a (biased) review of the state of the art of the Davydov/Scott model for energy transfer in proteins via the propagation of amide I excitations and of how this initial quantum stage may lead to protein conformational changes. It is not a traditional review because certain results reported in the literature have been complemented by extra simulations which revealed, for instance, a new class of possible states for the amide I excitation, here designated as double discrete breathers. The issue of the thermal stability of the Davydov soliton is discussed, as well as the deeper question of how to simulate the non-equilibrium regime of a mixed quantum-classical system at finite temperature. While an exact answer to the latter question is not yet available, a specific formalism that is able to reproduce the correct canonical ensemble is described. Finally, the question of how a quantum amide I excitation can generate of the specific protein conformational changes known to be associated with function is also explored. Indeed, computer simulations indicate that a local action can lead to reproducible conformational changes. The paper ends with a discussion of some of the open questions that plague/stimulate this field and with a suggestion for an experiment to test the basic assumption of the Davydov/Scott model.
Acknowledgement
This work received national funds from FCT – Foundation for Science and Technology, Portugal, through the project UID/Multi/04326/2013. The author also acknowledges the Laboratory for Advanced Computing at University of Coimbra (http://www.lca.uc.pt) for providing HPC computing resources that have contributed to the research results reported within this paper.
This article is dedicated to Professor Michael Springborg on the occasion of his 60th birthday. With best wishes for a long and happy scientific and personal life.
©2016 Walter de Gruyter Berlin/Boston
Articles in the same Issue
- Frontmatter
- Preface
- Congratulations to Michael Springborg
- Fourier Space Uncoupled Hartree–Fock Polarizabilities of One-Dimensionally Periodic Systems. Polyethylene and Polysilane Revisited
- Construction of Constrained Dipole Oscillator Strength Distributions
- Incremental DF-LCCSD(T) Calculations for a Water Molecule Inside and Outside Armchair Carbon Nanotubes
- An Efficient Unrestricted PCM-Elongation Method for Large High-Spin Polymer/Dendrimer Systems
- Variable van der Waals Radii Derived From a Hybrid Gaussian Charge Distribution Model for Continuum-Solvent Electrostatic Calculations
- Natural Extension of Hartree–Fock Through Extremal 1-Fermion Information: Overview and Application to the Lithium Atom
- Direct Piezoelectric Tensor of 3D Periodic Systems through a Coupled Perturbed Hartree–Fock/Kohn–Sham Method
- Intensive Atomization Energy: Re-Thinking a Metric for Electronic Structure Theory Methods
- The VES Hypothesis and Protein Conformational Changes
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- A First-Principles Study of Metal-Decorated Graphene Nanoribbons for Hydrogen Storage
- Defect Effects on the Interfacial Interactions between a (5, 5) Carbon Nanotube and an Al (111) Surface
- Structural Insight into Self Assembly of Sophorolipids: A Molecular Dynamics Simulation Study
- The Role of Mutations at the Side Door on the Thermal Stability and Structural Flexibility of the pnbCE Enzyme
- Electric (Hyper) Polarizability of the Hypofluorous Acid (HOF) from High-Level ab initio Calculations with Especially Designed Purpose-Oriented Basis Sets
- Conformational and Vibrational Analysis of 2-, 3- and 4-Pyridinecarbonyl Chloride Using DFT
- Spectral Properties of α and β L Rhamno-Indigo Molecules and Activities Prediction Through NBO Analysis. A DFT Study
- Solid State Structure Prediction Through DFT Calculations and 13C NMR Measurements: Case Study of Spiro-2,4-dithiohydantoins
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- Mn Adsorption on the GaAs(111)–(2×2)B Surface: First Principles Studies
- Charge and Compositional Effects on the 2D–3D Transition in Octameric AgAu Clusters
- Diversity Characterization of Binary Clusters by Means of a Generalized Distance
- First Principle Investigation of (Bi2O3)n Clusters With n = 6 − 9
- The Role of Aluminum Substitution on the Stability of Substituted Polyhedral Oligomeric Silsesquioxanes
- Ab-Initio Investigation of Nowotny Chimney Ladder Silicide Os2Si3 Using the Modified BJ Potential
- Surface Plasmon Assisted Two-Photon Ionization of Noble and Alkali Metal Clusters
- Temperature Dependence of Stability of Copper Clusters
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Articles in the same Issue
- Frontmatter
- Preface
- Congratulations to Michael Springborg
- Fourier Space Uncoupled Hartree–Fock Polarizabilities of One-Dimensionally Periodic Systems. Polyethylene and Polysilane Revisited
- Construction of Constrained Dipole Oscillator Strength Distributions
- Incremental DF-LCCSD(T) Calculations for a Water Molecule Inside and Outside Armchair Carbon Nanotubes
- An Efficient Unrestricted PCM-Elongation Method for Large High-Spin Polymer/Dendrimer Systems
- Variable van der Waals Radii Derived From a Hybrid Gaussian Charge Distribution Model for Continuum-Solvent Electrostatic Calculations
- Natural Extension of Hartree–Fock Through Extremal 1-Fermion Information: Overview and Application to the Lithium Atom
- Direct Piezoelectric Tensor of 3D Periodic Systems through a Coupled Perturbed Hartree–Fock/Kohn–Sham Method
- Intensive Atomization Energy: Re-Thinking a Metric for Electronic Structure Theory Methods
- The VES Hypothesis and Protein Conformational Changes
- Understanding the Electronic Structure of Graphene Quantum Dot-Fullerene Nanohybrids for Photovoltaic Applications
- A First-Principles Study of Metal-Decorated Graphene Nanoribbons for Hydrogen Storage
- Defect Effects on the Interfacial Interactions between a (5, 5) Carbon Nanotube and an Al (111) Surface
- Structural Insight into Self Assembly of Sophorolipids: A Molecular Dynamics Simulation Study
- The Role of Mutations at the Side Door on the Thermal Stability and Structural Flexibility of the pnbCE Enzyme
- Electric (Hyper) Polarizability of the Hypofluorous Acid (HOF) from High-Level ab initio Calculations with Especially Designed Purpose-Oriented Basis Sets
- Conformational and Vibrational Analysis of 2-, 3- and 4-Pyridinecarbonyl Chloride Using DFT
- Spectral Properties of α and β L Rhamno-Indigo Molecules and Activities Prediction Through NBO Analysis. A DFT Study
- Solid State Structure Prediction Through DFT Calculations and 13C NMR Measurements: Case Study of Spiro-2,4-dithiohydantoins
- Eu2+-Containing Luminescent Perovskite-Type Hydrides Studied by Electron Paramagnetic Resonance
- Mn Adsorption on the GaAs(111)–(2×2)B Surface: First Principles Studies
- Charge and Compositional Effects on the 2D–3D Transition in Octameric AgAu Clusters
- Diversity Characterization of Binary Clusters by Means of a Generalized Distance
- First Principle Investigation of (Bi2O3)n Clusters With n = 6 − 9
- The Role of Aluminum Substitution on the Stability of Substituted Polyhedral Oligomeric Silsesquioxanes
- Ab-Initio Investigation of Nowotny Chimney Ladder Silicide Os2Si3 Using the Modified BJ Potential
- Surface Plasmon Assisted Two-Photon Ionization of Noble and Alkali Metal Clusters
- Temperature Dependence of Stability of Copper Clusters
- Detecting and Quantifying Geometric Features in Large Series of Cluster Structures
