Soft Matter Systems for Biomedical Applications

Description

Preface Contents List of Contributors Part I Fundamentals of Soft Matter Systems 1 Water Contribution to the Protein Folding and Its Relevance in Protein Design and Protein Aggregation 1.1 Introduction 1.2 Hawley’s Theory 1.3 The Model for the Hydrated Protein 1.3.1 The Franzese-Stanley Coarse-Grained Water Model 1.3.2 The Coarse-Grained Hydration Water Model 1.3.3 The Coarse-Grained Protein-Water Model 1.4 Protein Design 1.4.1 Design Protocols 1.4.2 Design Results in Two Dimensions 1.4.3 Design Results in Three Dimensions 1.5 Protein Unfolding as a Precursor of Protein Aggregation 1.6 Conclusions References 2 Slow Dynamics of Biological Water 2.1 Introduction 2.2 Methods 2.3 Hydration Water 2.4 Slow Dynamics of Hydration Water Probed with Self Intermediate Scattering Functions 2.4.1 The α-relaxation of Hydration Water 2.4.2 The Long-Relaxation of Hydration Water and Its Connections to the Biomolecule Dynamics 2.5 Slow Dynamics of Hydration Water Probed with Self van Hove Correlation Functions 2.5.1 α-relaxation of Hydration Water and Cage-Escaping Hopping 2.5.2 Long-Relaxation of Hydration Water and Protein-Related Hopping 2.6 Conclusions References 3 Molecular Perspective on Solutions and Liquid Mixtures from Modelling and Experiment 3.1 Introduction 3.2 Classical Molecular Simulations 3.2.1 Force Fields 3.3 Structure of Molecular Liquids and Liquid Mixtures 3.3.1 Radial Distribution Functions 3.3.2 Spatial Distribution Functions 3.3.3 Cluster Analysis and H-Bonded Structures 3.4 Physical Observables 3.4.1 Density 3.4.2 Excess Molar Volume of Mixing 3.4.3 Excess Molar Enthalpy of Mixing 3.4.4 Viscosity 3.4.5 Translational Diffusion 3.4.6 Structure Factors 3.5 Case Studies 3.5.1 Unusual Density Variation 3.5.2 Excess Molar Enthalpies and Volumes of Alcohol Ether Mixtures and Their Dependence on the Clustering 3.5.3 Is the [PtCl6]2− Ion Preferentially Solvated by the Organic Solvent in a Water + Organic Solvent Solution? 3.5.4 The Low-Q Excess 3.5.5 Hydration of DNA Counterions 3.5.6 Is It Worth Trying to Calculate Viscosity for Ionic Liquids from Computer Simulations When the Experiments Fail? 3.6 Conclusions References 4 Lyotropic Liquid Crystal Phases of Phospholipids as Model Tools in Molecular Biophysics and Pharmacology 4.1 Introduction 4.2 General Properties of Phospholipid Membranes 4.2.1 Chemical Structure of Phospholipid Molecules 4.2.2 Phase Transitions of Phospholipid Membranes 4.3 Membranotropic Effects of Individual Drug Substances 4.3.1 Effects of Drug-Membrane Interactions 4.3.2 Molecular Aspects of Drug-Membrane Interactions 4.4 Membranotropic Effects of Drugs Combinations 4.4.1 Kosmotrope and Chaotrope Substances 4.4.2 Kinetics of Joint Drug-Membrane Interactions 4.5 Lipid Membranes Affected by External Factors: From Membranotropic Effects to Biomimetic Sensor Materials 4.5.1 Effects of Provitamin D Photo-Transformations on Thermodynamic Parameters of Model Lipid Membranes 4.5.2 Provitamin D Photo-Isomerisation in Cholesteric Liquid Crystals: Development of Sensor Materials for Bioequivalent Dosimetry of UV Radiation 4.6 Final Remarks and Perspectives References 5 Colloidal Particles in Confined and Deformed Nematic Liquid Crystals: Electrostatic Analogy and Its Implications 5.1 Introduction 5.2 Elastic Interactions in Nematic Liquid Crystal Colloids 5.3 Multipole Coefficients and Particle's Symmetry 5.3.1 Polar Anchoring 5.3.2 Azimuthal Anchoring and Chiral Colloids 5.4 Banana-Shaped Particles in a Nematic Cell 5.4.1 Homeotropic Cell 5.4.2 Planar Cell 5.5 Elastic Monopoles in a Nematic Cell 5.6 Colloidal Particles in a Deformed Nematic 5.7 Distribution of Nanoparticless in a Deformed Nematic 5.8 Coexistence of Two Colloidal Structures at the NLC-Air Interface 5.9 Conclusions References Part II Mechanisms and Molecular Interactions 6 DNA-Polyamine Interactions: Insight from Molecular Dynamics Simulations on the Sequence-Specific Binding of Spermidine3+ 6.1 Introduction 6.2 Features of DNA-Counterion Interactions 6.3 Molecular Dynamics Simulations of DNA with Polyamines 6.4 Distribution of Spermidine3+ Around DNA 6.5 Sequence Specificity of DNA-Polyamine Binding 6.6 DNA-DNA Interactions 6.7 Discussion and Conclusions References 7 The Influence of Sequence Dependence and External Solvents on DNA Conformation 7.1 Introduction 7.2 Methods 7.3 Influencing Factors of DNA Conformational Transition 7.3.1 Sequence Dependent-Induced DNA Conformational Transition 7.3.2 Distribution of Ions Around DNA 7.4 Configuration Transformation of DNA in Different Solvents 7.4.1 The Structural and Dynamic Properties of Alcohol Solvents 7.4.2 Alcohols Solvent and Low Activity Water Induced DNA Conformational Transitions 7.5 Conclusions References 8 Mechanisms of Heteroassociation of Ceftriaxone and Doxorubicin Drugs with Bovine Serum Albumin 8.1 Introduction 8.2 Preparation of Samples and Experimental Methods 8.3 Results and Discussion for Doxorubicin 8.3.1 Quantum Chemical Modeling of the Electronic Structure of Doxorubicin Molecules 8.3.2 Interaction in DOX-BSA Conjugates 8.3.3 Excitation Energy Transfer in the BSA-DOX System 8.3.4 Molecular Docking Study of the BSA-DOX Conjugates 8.3.5 Parameters of the Interaction in BSA-DOX Conjugates 8.3.6 Mechanisms of Intermolecular Interaction in BSA-DOX Conjugates 8.3.7 Conformational Transformations of BSA Macromolecules in Their Interaction with DOX Molecules 8.4 Results and Discussion for Ceftriaxone 8.4.1 Absorption Spectrum of Ceftriaxone 8.4.2 Molecular Docking Study of the BSA-Cef Conjugates 8.4.3 Nonradiative Transfer of Excitation Energy in the BSA-Cef Molecular System 8.4.4 Parameters of Intermolecular Interaction in the BSA-Cef System 8.4.5 Mechanisms of Intermolecular Interaction in the Aqueous Solutions of BSA-Cef 8.5 Conclusions References 9 Manifestation of Structural Isomerism in the Raman Spectra of Platinum Drugs 9.1 Introduction 9.2 Experimental Details 9.3 Structure and Vibrational Analysis 9.4 Symmetry, Prenormal Coordinates and Normal Vibrations of Cis- and Trans-Isomer Skeletons 9.5 Raman Spectra of Cisplatin and Transplatin 9.6 Conclusions References 10 Approaches for a Closer Look at Problems of Liquid Membranes with Amyloid-Beta Peptides 10.1 Introduction 10.2 Membrane Phase Transitions 10.3 Overall Membrane Thickness 10.4 Detailed Membrane Structure 10.5 Single Planar Membrane 10.6 Membrane Dynamics 10.7 Aβ Peptide Secondary Structure 10.8 Concluding Remarks References 11 Analysis of Natural and Engineered Amyloid Aggregates by Spectroscopic and Scattering Techniques 11.1 Introduction 11.2 Differences in the Origin of Natural Functional and Engineered Amyloids 11.3 Spectroscopic and Scattering Techniques for Fibril Analysis 11.3.1 Infrared Spectroscopy 11.3.2 Electron Paramagnetic Resonance Spectroscopy 11.3.3 Small Angle X-ray Scattering 11.4 Conclusion/Outlook References Part III Magnetic Field Effects 12 Liquid Biosystems in Gradient Magnetic Fields: Electrokinetic, Magnetophoretic and Orientation Effects 12.1 Magnetic Field Sources of Artificial and Biogenic Origin Acting on Biosystems 12.2 Magnetophoretic Effects in Liquid Biosystems 12.2.1 Magnetic Tweezers for Biomedical Applications 12.2.2 Phase Separation of Liquid Media Under Gradient Magnetic Fields 12.2.3 Magnetophoresis of the Internal Components of the Body. Biogenic Magnetic Nanoparticles as Magnetic Organelle 12.3 Electrokinetic Effects Under Gradient Magnetic Fields 12.4 Orientation Effects in Strong Magnetic Fields 12.5 Final Remarks and Future Perspectives References 13 Magnetic Fluids in Biosciences, Biotechnology and Environmental Technology 13.1 Introduction 13.2 Bioapplications of Magnetic Fluids 13.2.1 Magnetic Modification of Diamagnetic Materials 13.2.2 Synthesis of Magnetically Responsive Biobased and Related Materials 13.2.3 Separation of Biologically Active Compounds 13.2.4 Ferrofluid Modified (Bio)sorbents for Pollutant Removal 13.2.5 (Bio)analysis Using Ferrofluids and Ferrofluid-Modified Materials 13.2.6 Immobilization of Biologically Active Compounds and Cells on Ferrofluid-Modified Carriers 13.2.7 Other Biotechnology Applications of Ferrofluid Modified Materials 13.2.8 Peroxidase-Like Activity of Ferrofluid-Derived Materials 13.3 Conclusions References Part IV Nanosystems and Nanomaterials for Biomedical Applications 14 Smart Polymer-Based Multicomponent Nanosystem for Enhanced Anticancer Photodynamic Therapy 14.1 Introduction 14.2 Polymer Nanocarrier 14.3 Nanosystems for PDT 14.4 Methods Used for Nanosystems Study 14.5 In Vitro Experiments with Malignant Cells 14.6 Results and Discussion 14.7 Conclusions References 15 Biomedical Applications of Laponite®-Based Nanomaterials and Formulations 15.1 Introduction 15.2 Structure and Properties of Lap 15.2.1 Grades of Lap 15.2.2 Properties of Lap 15.2.3 Modified Lap 15.3 Drug Delivery Systems 15.3.1 Examples of Pharmaceutical Molecules 15.3.2 Nanoscale Drug Delivery Systems 15.4 Medical Lap-Based Hydrogels 15.4.1 Types and General Properties of Hydrogels 15.4.2 Gradient Hydrogels 15.4.3 Stimuli-Responsive Hydrogels 15.4.4 Medical Applications of Lap-Based Hydrogels 15.5 Cytotoxicity and Antimicrobial Activity Assessments 15.5.1 Toxicity Tests 15.5.2 Antimicrobial Tests 15.5.3 Examples of Bioactivity Assessments 15.6 Final Remarks and Perspectives References