Biophysics and Bioengineering
College 1 - An introduction to Biophysics and Bioengineering
Biophysics
Definitions:
- Biophysics – a branch of science concerned with the application of physical principles and
methods to biological problems
- Physics – a science that deals with matter and energy and their interactions
- Drug – a substance used to treat a dysfunctional human body (and other biological
organisms)
Relation ship physics to biological function → protein folding, carrying out biological functions
Bioengineering
Definitions
- Bioengineering; the application of engineering principles, practices and technologies to the
field of medicine and biology.
- Engineering:
o The application of science and mathematics by which the properties of matter and
the source of energy in nature are made useful to people
o The branch of science and technology concerned with the design, building, and use
of engines, machines and structures
Biophysics and bioengineering are growing!
College 2 – Molecular Biophysics for pharmaceutical sciences
Molecular biophysics consists of:
1. Structural biology (bulk analysis)
2. Single-molecule biophysics (single molecule)
Structural biology: Structural biology is a branch of biophysics concerned with the molecular
structure of biological macromolecules, especially proteins and nucleic acids
Why is it important? – Function of proteins and other biological macromolecules is intricately related
to their 3D shape and structure
Molecular structure of proteins:
1. Primary – Sequence (amino acids)
2. Secondary – Local folding (alpha helices and beta sheets)
3. Tertiary – Long range folding
4. Quaternary – multimeric organization
5. (Supramolecular – large-scale assemblies of macromolecules)
Landmarks in macromolecular structure determination
, - Watson & Crick – DNA helices structure
- Rosalind Franklin – X-Ry diffraction of DNA
- Dorothy Hodgkin – Structure of B12/Insulin
Tertiary protein structure: protein folding – Three main approaches
- Experimental determination (x-ray crystallography, protein NMR)
- Comparative modelling (based on homology)
- De novo prediction
X-ray crystallography
- Used to determine 80% of structures
- Requires high protein concentration
- Solubilization of the over-expressed protein
- Requires crystals
- Structure determination by diffraction of protein crystals
- Size of a molecule: no theoretical limit
Working principle of X-ray crystallography
1. Crystals act as 3D grating and produce diffraction
2. The diffraction pattern contains complete information on the placement of scatterers
(electrons in atoms)
3. By Fourier transformin the diffraction pattern, we can obtain information on the structure of
the molecule in the crystals
Nuclear magnetic resonance (NMR)
- Magnetic field applied to proteins in solution
- Does not require crystallization
- Solubilization of the over-expressed protein
- Structure determination of a molecule as it exists in solution
- Size-limit is a major factor
Pros NMR
➔ Provides high resolution information
➔ Does not require a crystal of protein and thus is not affected by crystal contacts
➔ Can be used to study flexible proteins
➔ Reflects conformational averaging
Cons NMR
➔ Requires high concentration of soluble proteins
➔ Can not be applied to large proteins – size limit is a major factor
➔ Cannot be used with amyloid fibrils
, Xray Vs NMR
➔ Producing enough proteins for trials Producing enough labelled protein
➔ Crystallization time and effort Size of a protein
➔ Assignment process is slow and error prone
Working principles NMR
1. Measures nuclear magnetism or changes in nuclear magnetism in a molecule
2. NMR spectroscopy measures the absorption of light due changes in nuclear spin orientation
3. NMR only occurs when a sample is in a strong magnetic field
4. Different nuclei absorb at different energies (frequencies)
Single-molecule biophysics
Why do we want to study single molecules?
- Bulk measurement: average of measured quantity is obtained
- Single molecules measurement: distribution of measured quantity is obtained
By averaging we may lose information.
Examples:
- An individual enzyme may exist in two or more states of activity that are not revealed by bulk
studies
➔ Static heterogeneity – different enzyme molecules function at different rates
➔ Dynamic heterogeneity – an enzyme molecule can switch between different rates
Single-molecule techniques
1. Atomic Force Microscopy (AFM)
2. Laser traps (Optical tweezers)
3. Single molecule fluorescence (FRET)
Atomic Force microscopy = a very high resolution type of
scanning probe microscopy. An AFM generates images by
scanning a small cantilever over the surface of a sample. The
sharp tip on the end of the cantilever contacts the surface,
bending the cantilever and changing the amount of laser light
reflected into the photodiode. The height of the cantilever is
then adjusted to restore the response signal resulting in the
measured cantilever height tracing the surface.
Advantages:
- Can achieve atomic resolution on hard, crystalline surfaces
- Can often achieve nanometre resolution on biological samples
- Imaging can be done in buffer – can image biological processes
- Can also be used to mechanically manipulated molecules
Different AFM modes:
College 1 - An introduction to Biophysics and Bioengineering
Biophysics
Definitions:
- Biophysics – a branch of science concerned with the application of physical principles and
methods to biological problems
- Physics – a science that deals with matter and energy and their interactions
- Drug – a substance used to treat a dysfunctional human body (and other biological
organisms)
Relation ship physics to biological function → protein folding, carrying out biological functions
Bioengineering
Definitions
- Bioengineering; the application of engineering principles, practices and technologies to the
field of medicine and biology.
- Engineering:
o The application of science and mathematics by which the properties of matter and
the source of energy in nature are made useful to people
o The branch of science and technology concerned with the design, building, and use
of engines, machines and structures
Biophysics and bioengineering are growing!
College 2 – Molecular Biophysics for pharmaceutical sciences
Molecular biophysics consists of:
1. Structural biology (bulk analysis)
2. Single-molecule biophysics (single molecule)
Structural biology: Structural biology is a branch of biophysics concerned with the molecular
structure of biological macromolecules, especially proteins and nucleic acids
Why is it important? – Function of proteins and other biological macromolecules is intricately related
to their 3D shape and structure
Molecular structure of proteins:
1. Primary – Sequence (amino acids)
2. Secondary – Local folding (alpha helices and beta sheets)
3. Tertiary – Long range folding
4. Quaternary – multimeric organization
5. (Supramolecular – large-scale assemblies of macromolecules)
Landmarks in macromolecular structure determination
, - Watson & Crick – DNA helices structure
- Rosalind Franklin – X-Ry diffraction of DNA
- Dorothy Hodgkin – Structure of B12/Insulin
Tertiary protein structure: protein folding – Three main approaches
- Experimental determination (x-ray crystallography, protein NMR)
- Comparative modelling (based on homology)
- De novo prediction
X-ray crystallography
- Used to determine 80% of structures
- Requires high protein concentration
- Solubilization of the over-expressed protein
- Requires crystals
- Structure determination by diffraction of protein crystals
- Size of a molecule: no theoretical limit
Working principle of X-ray crystallography
1. Crystals act as 3D grating and produce diffraction
2. The diffraction pattern contains complete information on the placement of scatterers
(electrons in atoms)
3. By Fourier transformin the diffraction pattern, we can obtain information on the structure of
the molecule in the crystals
Nuclear magnetic resonance (NMR)
- Magnetic field applied to proteins in solution
- Does not require crystallization
- Solubilization of the over-expressed protein
- Structure determination of a molecule as it exists in solution
- Size-limit is a major factor
Pros NMR
➔ Provides high resolution information
➔ Does not require a crystal of protein and thus is not affected by crystal contacts
➔ Can be used to study flexible proteins
➔ Reflects conformational averaging
Cons NMR
➔ Requires high concentration of soluble proteins
➔ Can not be applied to large proteins – size limit is a major factor
➔ Cannot be used with amyloid fibrils
, Xray Vs NMR
➔ Producing enough proteins for trials Producing enough labelled protein
➔ Crystallization time and effort Size of a protein
➔ Assignment process is slow and error prone
Working principles NMR
1. Measures nuclear magnetism or changes in nuclear magnetism in a molecule
2. NMR spectroscopy measures the absorption of light due changes in nuclear spin orientation
3. NMR only occurs when a sample is in a strong magnetic field
4. Different nuclei absorb at different energies (frequencies)
Single-molecule biophysics
Why do we want to study single molecules?
- Bulk measurement: average of measured quantity is obtained
- Single molecules measurement: distribution of measured quantity is obtained
By averaging we may lose information.
Examples:
- An individual enzyme may exist in two or more states of activity that are not revealed by bulk
studies
➔ Static heterogeneity – different enzyme molecules function at different rates
➔ Dynamic heterogeneity – an enzyme molecule can switch between different rates
Single-molecule techniques
1. Atomic Force Microscopy (AFM)
2. Laser traps (Optical tweezers)
3. Single molecule fluorescence (FRET)
Atomic Force microscopy = a very high resolution type of
scanning probe microscopy. An AFM generates images by
scanning a small cantilever over the surface of a sample. The
sharp tip on the end of the cantilever contacts the surface,
bending the cantilever and changing the amount of laser light
reflected into the photodiode. The height of the cantilever is
then adjusted to restore the response signal resulting in the
measured cantilever height tracing the surface.
Advantages:
- Can achieve atomic resolution on hard, crystalline surfaces
- Can often achieve nanometre resolution on biological samples
- Imaging can be done in buffer – can image biological processes
- Can also be used to mechanically manipulated molecules
Different AFM modes:
