Structure and function of cytochromes / Elaine J. Mathis, editor.

Format:

Book

Contributor:

Mathis, Elaine J., editor.

Series:

Biochemistry and Molecular Biology in the Post Genomic Era

Language:

English

Subjects (All):

Cytochromes.

Cytochromes--Analysis.

Physical Description:

1 online resource (296 pages)

Edition:

1st ed.

Place of Publication:

New York, NY : Nova Science Publishers, Inc., [2022]

Summary:

"This book contains five chapters exploring the structure and function of cytochromes, which are redox-active proteins that contain a heme with a central Fe atom at its core as a cofactor. Chapter One explores the functional relevance of cytochrome c-oxidase subunit IV isoform expression for cellular energy sensing, ATP production, and oxidative stress levels and its role in neurodegeneration. Chapter Two deals with the factors determining the orientation of ligated histadines in hemoproteins, cytochromes, and model systems. Chapters Three and Four include comparative studies of native and synthetic cytochrome b. Lastly, Chapter Five discusses some examples of synthetic and native cytochromes used as central components of biosensors in bioelectronic/biocatalytic applications"-- Provided by publisher.

Contents:

Intro

Contents

Preface

Chapter 1

Cytochrome C-Oxidase as a Neuroprotective Target

Abstract

CCO Structure, Evolution and Biochemistry across Species

The Evolution of CCO

CCO Isoforms

Relevant Mutations in CCO

The Proton Pumping of the Cytochrome C-Oxidase

The Proton Pumping Stoichiometry

The Proton Pumping Function

The Role of CCO in Neurodegeneration

Alzheimer's Disease

Parkinson's Disease

Huntington's Disease

Amyotrophic Lateral Sclerosis

The Therapeutic Potential of Targeting CCO

Estrogen Is Neuroprotective through Modulation of CCO Dynamics

Targeting CCO to Reduce Metal Accumulation

CCO as a Neuroprotector against Hypoxia

CCO, Insulin and Neuroprotection

Novel Therapeutics in CCO

CCO Promising Therapies

Identifying the Therapeutic Dosage

CCO as a Rescue Factor in Neurodegeneration

Conclusion

References

Chapter 2

Factors Determining the Orientation

of Ligated Histidines in Hemoproteins, Cytochromes, and Model Systems

Abbreviations

Introduction

Method

Data Mining in the PDB

Characterizing the Orientation of Ligated Imidazole Relative to Heme

Characterizing Hydrogen Bonds Involving Imidazole Axially Ligated to Heme

Molecular Force Field Computations

Quantum-Chemical Computations

Computation of the Solution-Phase Energy by One-Step Procedure

Computation of Atomic Partial Charges

Computation of Solvation Energy

Solvent Probe Radius

Modeling of Propionic Group Interaction

Computation of Dipole Moment

Results and Discussion

General Overview of PDB Data

Role of Propionic Acids

Analyzing Data from the PDB

Force Field Computations

DFT Computations

Imidazole-Heme Conformation in Vacuum

Imidazole-Heme Conformation in a Dielectric Continuum: The One-Step Procedure.

Imidazole-Heme Conformation in A Dielectric Continuum: The Two-Step Procedure

Electron Leakage

Influence of histidine backbone

Imidazole-Heme Conformations for Different Groups of Heme Proteins

Analyzing data from the PDB

Cytochrome c Groups

Myoglobin and Hemoglobin Groups

Cytochrome b Group

Cytochrome c Peroxidase Group

Mutual Orientation of Two Axially Coordinated Histidines

Hydrogen Bonding Scheme of Imidazole Ligated to Heme

H-Bonds of Axially Coordinated Imidazoles in Myoglobin and Hemoglobin

Mb

Hb

H-Bonds of Axially Ligated Imidazoles in Cytochrome c Peroxidase

H-Bonds of Axially Ligated Imidazoles in Mono-Histidine Ligated Cytochrome c

Mono-Cc124

Mono-Cc6

Mono-Cc'

H-Bonds of Axially Ligated Imidazoles in Bis-Histidine Ligated Cytochromes

Influence of H-Bonds on Imidazole Orientation in Heme Proteins

Possible H-Bonds of Imidazoles Axially Ligated to Heme in Heme Proteins

Acknowledgments

Biographical Sketches

Chapter 3

Comparative Study on Structure-Function Correlation of Native and Synthetic Cytochrome b: Protonation and

Redox Properties

Material and Method

Titration Curves of Ionizable Groups

Acid-Base Equilibrium of a Single Titratable Group

Redox Equilibrium of a Single Redox-Active Group

The Model of a Protein in Solution

Continuum Electrostatic Method

The pKa and E0 Calculations in Proteins

The Poisson-Boltzmann Equation

The Boltzmann Sum and Protonation/Redox State Energy

Definition of pKa and E0 of Ionizable Groups in a Protein Environment

Dielectric Constant

Computational Models

Titratable Groups

Atomic Partial Charges.

Preparation of Structures for Electrostatic Computations

Calculations on the Synthetic Cytochrome b

Protonation Pattern of Titratable Groups

Calculated pH-Dependent Heme Redox Potentials

Role of the Phe and Trp and the Electrostatic Coupling of the Hemes

Effect of Dielectric Medium and Specific Charge Distribution

Influence of Different Residues on the Redox Potentials

Calculations on the Native Cytochrome b

Experimental Values of the Heme Redox Potentials

Calculated Redox Potentials in the Whole Cytbc1 Complex

Calculated Redox Potentials of the Hemes in the Cytb Subunit

Redox Titrations

The Coupling of Protonation and Redox Reactions

The Effects of Ionic Strength, External Redox Potential, and the Redox-Bohr Effect

Chapter 4

Comparative Study of Native and Synthetic Cytochrome b: Modeling, Dynamics, and Bioinformatics Study

Molecular Mechanics Force Field

Molecular Dynamics

Respiratory Electron Transport Chain

Coupling of Oxidative Phosphorylation to the Electron Transport

Electron Transport

The Sequence of Electron Transport

Complex III

Molecular Modeling

Protein Design

Generation of Atomic Coordinates

Preparation of the Native Cytb Subunit for MD Simulation

Molecular Dynamics Simulation

Molecular Modeling and Bioinformatics Study

Structural Relaxation of the SynCytb

Salt Bridges in the SynCytb

Comparison of Heme Conformations in Synthetic and Native Cytb

The Relative Orientation of the Hemes and Tilted Helices

Experimental Data

Molecular Dynamics Study

Stability of the Synthetic and Native Cytb.

RMS Fluctuations of the Synthetic and Native Cytb

Chapter 5

Redox Properties of Small Synthetic Hemoproteins and Native Enzymes for Application in Bionanotechnology and Bioelectronic Devices

Design of Novel Proteins

Biosensors and Bioelectronic Devices Based on Native and Artificial Cytochromes

Enzyme Electrodes and Electrochemical Detection

Bifunctional Synthetic Redox-Active Protein Electrode

Bioelectrocatalytical Cytochrome c/Cytochrome c Oxidase Electrode

Biosensors and Biomolecular Recognition

Studied Models

Redox Potential Calculations

Heme Orientation in the Helix-Bundle

Protonation State and Effects of Ionizable Groups

Comparison of Calculated vs. Measured Em

General Findings

Index

Blank Page.

Notes:

Description based on print version record.

Other Format:

Print version: Mathis, Elaine J. Structure and Function of Cytochromes

ISBN:

9798886971224