Research Methods in Biomineralization Science

Research Methods in Biomineralization Science

1st Edition - September 15, 2013
This is the Latest Edition
  • Editor: Jim De Yoreo
  • Hardcover ISBN: 9780124166172
  • eBook ISBN: 9780124166554

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Description

This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in biomineralization science, and includes sections on such topics as determining solution chemistry, structure and nucleation; probing structure and dynamics at surfaces; and interfaces mapping biomineral and morphology and ultrastructure.

Key Features

  • Continues the legacy of this premier serial with quality chapters authored by leaders in the field
  • Covers research methods in biomineralization science
  • Contains sections on such topics as and includes sections on such topics as determining solution chemistry, structure and nucleation; probing structure and dynamics at surfaces; and interfaces mapping biomineral and morphology and ultrastructure

Readership

Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists.

Table of Contents

  • Series Page

    Contributors

    Preface

    Methods in Enzymology

    Section I: Investigating Solution Chemistry, Structure, and Nucleation

    Chapter One. Development of Accurate Force Fields for the Simulation of Biomineralization

    Abstract

    1 Introduction

    2 Force Field Selection and Refinement

    3 The Mineral–Aqueous Interface

    4 Organics in Geochemical Systems

    5 Summary

    Acknowledgments

    References

    Chapter Two. The Integration of Ion Potentiometric Measurements with Chemical, Structural, and Morphological Analysis to Follow Mineralization Reactions in Solution

    Abstract

    1 Introduction

    2 Ion Potentiometric Measurements

    3 Combination of Ion Potentiometric Measurements with other Analysis Techniques

    4 Comparison with Standard Analyses

    5 Summary

    References

    Chapter Three. Investigating the Early Stages of Mineral Precipitation by Potentiometric Titration and Analytical Ultracentrifugation

    Abstract

    1 Introduction

    2 Equipment

    3 Experimental Procedures

    4 Data Evaluation

    5 Conclusions and Outlook

    References

    Chapter Four. Replica Exchange Methods in Biomineral Simulations

    Abstract

    1 Introduction

    2 Monte Carlo Sampling

    3 Replica Exchange MD

    4 Application of REMD to Early Stage Mineralization

    5 Summary

    References

    Chapter Five. SAXS in Inorganic and Bioinspired Research

    Abstract

    1 Introduction

    2 General Considerations: How Does SAXS/WAXS Work and When It Is Applicable?

    3 What Happens in a Solution When Ions Meet and How Do We Quantify it?

    4 SAXS Data Processing and Interpretation

    5 Case Studies

    6 Outlook

    Acknowledgments

    References

    Chapter Six. In Situ Solution Study of Calcium Phosphate Crystallization Kinetics

    Abstract

    1 Introduction

    2 Solution Preparation and Experimental Considerations

    3 In Situ Experiments

    4 Data Handling/Processing

    5 Summary

    References

    Section II: Probing Structure and Dynamics at Surfaces and Interfaces

    Chapter Seven. Design, Fabrication, and Applications of In Situ Fluid Cell TEM

    Abstract

    1 Introduction

    2 Fluid Cell Design

    3 Cell Fabrication and Assembly

    4 TEM Operation

    5 Effects of the Electron Beam on Reactions in the Fluid Cell

    6 Conclusions

    Acknowledgments

    References

    Chapter Eight. X-ray Absorption Spectroscopy for the Structural Investigation of Self-Assembled-Monolayer-Directed Mineralization

    Abstract

    1 Introduction

    2 Theory

    3 Experimental

    4 Analysis

    Acknowledgments

    References

    Chapter Nine. Cryo-TEM Analysis of Collagen Fibrillar Structure

    Abstract

    1 Introduction

    2 Sample Preparation for Cryo-TEM

    3 Image Acquisition and Processing

    4 Image Averaging

    5 Summary and Outlook

    Acknowledgments

    References

    Section III: Biomimetic Crystallization Techniques in vitro

    Chapter Ten. Preparation of Organothiol Self-Assembled Monolayers for Use in Templated Crystallization

    Abstract

    1 Introduction

    2 Crystallization Approaches Using SAMs as Templates

    3 Preparation

    4 Why Good SAMs Go Bad

    5 SAM Preparation Procedure

    6 Summary

    Acknowledgments

    References

    Chapter Eleven. Experimental Techniques for the Growth and Characterization of Silica Biomorphs and Silica Gardens

    Abstract

    1 Introduction

    2 Silica Biomorphs

    3 Chemical Gardens

    4 Conclusions and Outlook

    Acknowledgments

    References

    Chapter Twelve. Precipitation in Liposomes as a Model for Intracellular Biomineralization

    Abstract

    1 Introduction

    2 Model Systems for Studying the Influence of Confinement on Biomineralization

    3 Preparation of Liposomes

    4 Precipitation Inside Liposomes

    5 Characterization Methods

    6 Conclusions

    Acknowledgments

    References

    Chapter Thirteen. Polymer-Mediated Growth of Crystals and Mesocrystals

    Abstract

    1 Introduction

    2 Insoluble Polymers

    3 Soluble Polymers

    4 Conclusion

    References

    Chapter Fourteen. Phage Display for the Discovery of Hydroxyapatite-Associated Peptides

    Abstract

    1 Introduction

    2 Methods

    3 Summary

    References

    Section IV: Protein Structure, Interactions and Function

    Chapter Fifteen. Quantitatively and Kinetically Identifying Binding Motifs of Amelogenin Proteins to Mineral Crystals Through Biochemical and Spectroscopic Assays

    Abstract

    1 Introduction

    2 Strategy and Rationale

    3 Experimental Components and Considerations

    4 Experimental Approaches

    5 Data Handling and Processing

    6 Summary

    Acknowledgments

    References

    Chapter Sixteen. Using the RosettaSurface Algorithm to Predict Protein Structure at Mineral Surfaces

    Abstract

    1 Introduction

    2 Algorithm Evolution and Prior Results

    3 Computational Methods

    4 Protocol Capture

    5 Future Challenges

    Acknowledgments

    References

    Chapter Seventeen. Investigating Protein Function in Biomineralized Tissues Using Molecular Biology Techniques

    Abstract

    1 Introduction

    2 Discovery of Proteins Involved in Biomineralization

    3 Analysis of Function

    Acknowledgments

    References

    Section V: Mapping Biomineral Morphology and Ultrastructure

    Chapter Eighteen. Imaging the Nanostructure of Bone and Dentin Through Small- and Wide-Angle X-Ray Scattering

    Abstract

    1 Introduction

    2 Experimental Setup

    3 Overview of Parameters

    4 Treatment of SAXS Data from Mineralized Tissue

    5 Treatment of WAXD Data from Mineralized Tissues

    6 Analysis Tools

    7 Combination of Scanning SAXS/WAXD with Other Methods

    8 Conclusions

    References

    Chapter Nineteen. Synchrotron X-Ray Nanomechanical Imaging of Mineralized Fiber Composites

    Abstract

    1 Introduction

    2 Molecular and Nanoscale Strains and Stresses in a Prototypical Biomineralized Composite

    3 Relation between X-Ray Spectra and Nanomechanics

    4 Sample Preparation for In Situ Mechanical Testing with Synchrotron X-Rays

    5 Mechanical Tester Design

    6 Synchrotron Setup

    7 In Situ Experimental Procedure

    8 Data Analysis

    9 Case Studies

    10 Model Interpretation

    11 Summary

    Acknowledgments

    References

    Section VI: Mapping Mineral Chemistry

    Chapter Twenty. Application of Total X-Ray Scattering Methods and Pair Distribution Function Analysis for Study of Structure of Biominerals

    Abstract

    1 Introduction

    2 Total Scattering Methodology

    3 The PDF

    4 Extracting Information from the PDF

    5 PDF Studies of Biominerals

    6 Summary

    Links

    Acknowledgments

    References

    Chapter Twenty-One. X-Ray Microdiffraction of Biominerals

    Abstract

    1 Introduction

    2 Elements of X-Ray (Micro)Diffraction

    3 Synchrotron, X-Ray Focusing Optics, and Area Detectors

    4 Sample Preparation

    5 Powder X-Ray Microdiffraction

    6 White-Beam X-Ray Microdiffraction

    7 Microbeam Small-Angle X-Ray Scattering

    8 Future Developments

    References

    Chapter Twenty-Two. FTIR and Raman Studies of Structure and Bonding in Mineral and Organic–Mineral Composites

    Abstract

    1 Introduction

    2 FTIR and Raman Spectroscopies Overview

    3 The Raman Effect

    4 Measuring Biomimetic Crystals and Biominerals

    5 Future Directions

    Acknowledgments

    References

    Chapter Twenty-Three. A Mixed Flow Reactor Method to Synthesize Amorphous Calcium Carbonate Under Controlled Chemical Conditions

    Abstract

    1 Introduction

    2 Method

    3 Characterization

    4 Results

    References

    Author Index

    Subject Index

Product details

  • No. of pages: 704
  • Language: English
  • Copyright: © Academic Press 2013
  • Published: September 15, 2013
  • Imprint: Academic Press
  • Hardcover ISBN: 9780124166172
  • eBook ISBN: 9780124166554

About the Serial Volume Editor

Jim De Yoreo