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Intro; Preface; Contents; 1 Physical Methods for Studying Proteins; 1.1 Electrophoresis Methods; 1.2 Chromatographic Methods; 1.3 Mass Spectrometry; 1.3.1 Electron Impact; 1.3.2 Chemical Ionization; 1.4 X-ray Analysis of Protein Crystals; 1.5 Methods of Spectral Analysis; 1.5.1 Spectroscopy in the Ultraviolet and Visible Range; 1.6 Spectrofluorimetry; 1.7 Circular Dichroism; 1.8 Conclusion; References; 2 Mathematical Simulation of Complex Formation of Protein Molecules Allowing for Their Domain Structure; 2.1 Introduction; 2.2 General Principles of the Formation of Biological Complexes
2.2.1 Formation of Heterodimers (H3-H4) and (H2A-H2B)2.3 Description of the Physical Model; 2.4 The Problem of the Electrostatic Interaction of Two Conducting Spheres; 2.5 Physical Interpretation of Condition Number; 2.6 Numerical Simulation of Interaction of Biological Systems. Conclusion; 2.6.1 Heterodimer Formation H2A-H2B; 2.6.2 Heterodimer Formation H3-H4; 2.7 MATLAB Script for Mathematical Simulation of Complex Formation of Protein Molecules Allowing for Their Domain Structure; References
3 Mathematical Modelling of the Temperature Effect on the Character of Linking Between Monomeric Proteins in Aqueous Solutions3.1 Introduction; 3.2 The Main Properties of Proteins and the Nature of Their Behavior with Increasing Temperature; 3.3 The Physical Properties of the Studied Proteins H2A, H2B, H3, H4, Bcl-xl; 3.4 Description of the Physical Model; 3.5 Numerical Modelling of the Effect of Temperature on the Character of Binding of Monomeric Proteins to Aqueous Solutions. Conclusion
3.6 Matlab Script for Mathematical Modelling of the Temperature Effect on the Character of Linking Between Monomeric Proteins in Aqueous SolutionsReferences; 4 Mathematical Modelling of the Effect of a Monovalent Salt Solution on the Interaction of Protein Molecules; 4.1 Introduction; 4.2 General Principles for the Formation of Dimers H2A-H2B, H3-H4 and the Behavior of These Compounds in Solutions with Different Concentrations of Monovalent Salt; 4.3 Shielding Effect in a Salt Solution; 4.3.1 Debye Length; 4.4 Description of the Physical Model; 4.5 Results of Numerical Simulation. Conclusion
4.6 Matlab Script for Mathematical Modelling of the Effect of a Monovalent Salt Solution on the Interaction of Protein MoleculesReferences; 5 Mathematical Modeling Identification of Active Sites Interaction of Protein Molecules; 5.1 Introduction; 5.2 The Structure and Function of the Protein P53; 5.3 The Structure and Functions of the Protein Mdm2; 5.4 The Structure and Functions of the Protein Nap1; 5.5 Description of the Algorithms; 5.5.1 Algorithm 1; 5.5.2 Algorithm 2; 5.6 Numerical Simulation of the Formation of Heterodimers and Homodimers According to Algorithm 1
2.2.1 Formation of Heterodimers (H3-H4) and (H2A-H2B)2.3 Description of the Physical Model; 2.4 The Problem of the Electrostatic Interaction of Two Conducting Spheres; 2.5 Physical Interpretation of Condition Number; 2.6 Numerical Simulation of Interaction of Biological Systems. Conclusion; 2.6.1 Heterodimer Formation H2A-H2B; 2.6.2 Heterodimer Formation H3-H4; 2.7 MATLAB Script for Mathematical Simulation of Complex Formation of Protein Molecules Allowing for Their Domain Structure; References
3 Mathematical Modelling of the Temperature Effect on the Character of Linking Between Monomeric Proteins in Aqueous Solutions3.1 Introduction; 3.2 The Main Properties of Proteins and the Nature of Their Behavior with Increasing Temperature; 3.3 The Physical Properties of the Studied Proteins H2A, H2B, H3, H4, Bcl-xl; 3.4 Description of the Physical Model; 3.5 Numerical Modelling of the Effect of Temperature on the Character of Binding of Monomeric Proteins to Aqueous Solutions. Conclusion
3.6 Matlab Script for Mathematical Modelling of the Temperature Effect on the Character of Linking Between Monomeric Proteins in Aqueous SolutionsReferences; 4 Mathematical Modelling of the Effect of a Monovalent Salt Solution on the Interaction of Protein Molecules; 4.1 Introduction; 4.2 General Principles for the Formation of Dimers H2A-H2B, H3-H4 and the Behavior of These Compounds in Solutions with Different Concentrations of Monovalent Salt; 4.3 Shielding Effect in a Salt Solution; 4.3.1 Debye Length; 4.4 Description of the Physical Model; 4.5 Results of Numerical Simulation. Conclusion
4.6 Matlab Script for Mathematical Modelling of the Effect of a Monovalent Salt Solution on the Interaction of Protein MoleculesReferences; 5 Mathematical Modeling Identification of Active Sites Interaction of Protein Molecules; 5.1 Introduction; 5.2 The Structure and Function of the Protein P53; 5.3 The Structure and Functions of the Protein Mdm2; 5.4 The Structure and Functions of the Protein Nap1; 5.5 Description of the Algorithms; 5.5.1 Algorithm 1; 5.5.2 Algorithm 2; 5.6 Numerical Simulation of the Formation of Heterodimers and Homodimers According to Algorithm 1