Part i lecture 10 applications to biophysics and bionanomechanics

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Biological systems (simulation in biophysics) – how proteins work and how to model them ... lecture 10: applications to biophysics and bionanomechanics ...

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Table of contents
Table of contents
Content overview
2
    Overview: Material covered so far…
    3
      Lecture 10: Applications to biophysics and bionanomechanics
      4
        1. Force fields for organic chemistry - how to model proteins
        5
          Significance of proteins
          6
            Human body: Composed of diverse array of protein materials
            7
              Cellular structure: Protein networks
              8
                Protein structures define the cellular architecture
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                  How protein materials are made – the genetic code
                  10
                    Chemical structure of peptides/proteins
                    11
                      There are 20 natural amino acids Difference in side chain, R
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                        Chemistry, structure and properties are linked
                        13
                          Concept: split energy contributions
                          14
                            Force fields for organics: Basic approach
                            15
                              Force fields for organics: Basic approach
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                                Force fields for organics: Basic approach
                                18
                                  H-bond model
                                  19
                                    Summary
                                    20
                                      The need for atom typing
                                      21
                                        Atom typing in CHARMM
                                        22
                                          VMD analysis of protein structure
                                          23
                                            Common empirical force fields for organics and proteins
                                            24
                                              CHARMM force field
                                              25
                                                Application – protein folding
                                                26
                                                  Movie: protein folding with CHARMM
                                                  27
                                                    Movies in equilibrium (temperature 300 K)
                                                    28
                                                      2. Single molecule mechanics
                                                      29
                                                        Cooking spaghetti
                                                        30
                                                          Single molecule tensile test – “optical tweezer”
                                                          31
                                                            Example 1: Elasticity of tropocollagen molecules
                                                            32
                                                              Example 2: Single protein molecule mechanics
                                                              33
                                                                Example 3: Single DNA molecule mechanics
                                                                34
                                                                  Structural makeup of protein materials
                                                                  35
                                                                    How protein materials are made–the genetic code
                                                                    36
                                                                      Alpha-helix (abbreviated as AH)
                                                                      37
                                                                        Primary, secondary, tertiary structure
                                                                        38
                                                                          Beta-sheets (abbreviated as BS)
                                                                          39
                                                                            Amyloid proteins (Alzheimer’s disease)
                                                                            40
                                                                              3. Fracture of protein domains – Bell model
                                                                              41
                                                                                How to apply load to a molecule
                                                                                42
                                                                                  Steered molecular dynamics (SMD)
                                                                                  43
                                                                                    Steered molecular dynamics (SMD)
                                                                                    44
                                                                                      SMD is a useful approach to probe the nanomechanics of proteins (elastic deformation, “plastic” – permanent deformation, etc.)
                                                                                      46
                                                                                        Protein unfolding - ReaxFF
                                                                                        48
                                                                                          Comparison – CHARMM vs. ReaxFF
                                                                                          50
                                                                                            Application to alpha-helical proteins
                                                                                            51
                                                                                              Vimentin intermediate filaments
                                                                                              52
                                                                                                Intermediate filaments – occurrence
                                                                                                54
                                                                                                  Alpha-helical protein: stretching
                                                                                                  55
                                                                                                    What about varying pulling speeds?
                                                                                                    56
                                                                                                      Variation of pulling speed
                                                                                                      57
                                                                                                        Force at angular point fAP=fracture force
                                                                                                        58
                                                                                                          General results…
                                                                                                          59
                                                                                                            Rupture force vs. pulling speed
                                                                                                            60
                                                                                                              How to make sense of these results?
                                                                                                              61
                                                                                                                A few fundamental properties of bonds
                                                                                                                62
                                                                                                                  Bell model
                                                                                                                  63
                                                                                                                    Bell model
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                                                                                                                      Bell model
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                                                                                                                        Bell model
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                                                                                                                          Bell model
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                                                                                                                            Bell model
                                                                                                                            68
                                                                                                                              Bell model
                                                                                                                              69
                                                                                                                                Structure-energy landscape link
                                                                                                                                70
                                                                                                                                  Bell model
                                                                                                                                  71
                                                                                                                                    Bell model
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                                                                                                                                      Bell model
                                                                                                                                      73
                                                                                                                                        Simplification and grouping of variables
                                                                                                                                        74
                                                                                                                                          Bell model
                                                                                                                                          75
                                                                                                                                            behavior of strength
                                                                                                                                            76
                                                                                                                                              Scaling with Eb : shifts curve
                                                                                                                                              77
                                                                                                                                                Scaling with xb: changes slope
                                                                                                                                                78
                                                                                                                                                  Simulation results
                                                                                                                                                  79
                                                                                                                                                    Mechanisms associated with protein fracture
                                                                                                                                                    80
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                                                                                                                                                      11.021, 3.021, 10.333, 22.00Introduction to Modeling and SimulationSpring 2011Part I –Continuum and particle methodsMarkus J. BuehlerLaboratory for Atomistic and Molecular MechanicsDepartment of Civil and Environmental EngineeringMassachusetts Institute of TechnologyApplications to biophysics and bionanomechanics Lecture 10 2Content overviewI. Particle and continuum methods1.Atoms, molecules, chemistry2.Continuum modeling approaches and solution approaches 3.Statistical mechanics4.Molecular dynamics, Monte Carlo5.Visualization and data analysis 6.Mechanical properties –application: how things fail (and how to prevent it)7.Multi-scale modeling paradigm8.Biological systems (simulation in biophysics) –how proteins work and how to model themII. Quantum mechanical methods1.It’s A Quantum World: The Theory of Quantum Mechanics2.Quantum Mechanics: Practice Makes Perfect3.The Many-Body Problem: From Many-Body to Single-Particle4.Quantum modeling of materials5.From Atoms to Solids6.Basic proper...

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