Chemical Biology
LECTURES SUMMARY
Doorslaer, R.F.J.F. Van
TU EINDHOVEN BMT | 23-04-2018
,TABLE OF CONTENTS
College 1: 23-04-2018 ...................................................................................... 3
tentamen........................................................................................................ 3
Structural biology ................................................................................................ 3
Intrinsically disordered proteins ............................................................................ 3
X-ray and nmr .................................................................................................. 3
protein structure elucidation ................................................................................... 3
x-ray crystallography .......................................................................................... 3
nuclear magnetic resonance (nmr) ......................................................................... 4
proteins ......................................................................................................... 4
Protein crystallization ........................................................................................ 4
case study: control of epigenetics by bromodomain inhibitors ........................................... 5
College 2: 23-04-2018 ...................................................................................... 7
proteins ............................................................................................................ 7
Protein domains................................................................................................ 7
College 3: 30-04-2018 .................................................................................... 10
Signal transduction 1 .......................................................................................... 10
Receptor tyrosine kinases (RTK) .......................................................................... 10
chemical induced dimerization ............................................................................ 11
College 4: 02-05-2018 .................................................................................... 14
Signal transduction 2 .......................................................................................... 14
Receptor tyrosine kinases .................................................................................. 14
g protein coupled receptors ............................................................................... 15
College 5: 07-05-2018 .................................................................................... 18
enzymes and protein profiling (abpp) ....................................................................... 18
College 6: 14-05-2018 .................................................................................... 21
labeling of proteins, assays and hts ......................................................................... 21
College 7: 17-05-2018 .................................................................................... 24
dna: synthesis, sequencing, therapy (h3) .................................................................. 24
College 8: 24-05-2018 .................................................................................... 26
14-3-3 protein-protein interaction .......................................................................... 26
College 9: 28-05-2018 .................................................................................... 27
Protein engineering ............................................................................................ 27
Rational approach ........................................................................................... 27
combinational approach .................................................................................... 27
evolution ...................................................................................................... 28
College 10: 31-05-2018 ................................................................................. 29
, microfluidics .................................................................................................... 29
College 12: 07-06-2018 ................................................................................. 31
Clinical chemistry .............................................................................................. 31
lung cancer & liquid biopsy ................................................................................ 31
College 13: 11-06-2018 ................................................................................. 32
Chemical synthesis of peptides chapter 5 .................................................................. 32
Amino acid nomenclature and properties ............................................................... 32
amide coupling reagents and peptide synthesis ........................................................ 32
spss............................................................................................................. 33
guided selfstudies ................................................................................................. 34
‘100 years of crystallography’ ................................................................................ 34
Phospho-Ser/Thr-binding domains ........................................................................... 36
‘Chemical Induced Dimerization’ ............................................................................ 38
“Small-molecule inhibitors of the interaction between TNF and TNFR“ .............................. 40
‘Enzymes, Kinases, Proteases, Activity-Based Protein Profiling’ ....................................... 42
Fluorophores, Protein Labeling, HTS ........................................................................ 44
“DNA” ............................................................................................................ 46
“Chemical Biology of 14-3-3 proteins” ...................................................................... 47
“peptide synthesis” ............................................................................................ 49
, COLLEGE 1: 23-04-2018
- Chemical Biology is the manipulation of biological systems.
- Gene lockouts are black and white switches, they either are active or not, RNAi is used to
control this.
TENTAMEN
- Learn Nobel prizes.
- Learn amino acids with their characteristic groups identify those in electron cloud
image.
- Rigidity: what are the most important factors in rigidity as anchoring principle/interaction
with protein pockets?
STRUCTURAL BIOLOGY
INTRINSICALLY DISORDERED PROTEINS
These proteins are incorrectly folded and measure up to 30-40% of the total amount of proteins
present in our bodies. They cause 60-70% of all diseases and are therefore important to target with
medicines. They do not have nicely folded 3D structures as normal proteins but their structure
fluctuates. What is special, is that their function depends on this fluctuation in structure.
IDP’s do not have binding pockets and can take on toxic forms.
An important example is the drug for Alzheimer’s disease: Tau. This protein is very difficult to
target by reasons stated above and is therefore hard to treat when Tau takes on a dangerous
structure to the brain.
X-RAY AND NMR
- CD, Fluorescence spectroscopy and Mass spectroscopy are also used, however, X-ray and
NMR are the most common.
PROTEIN STRUCTURE ELUCIDATION
X-RAY CRYSTALLOGRAPHY
Principles:
- Crystals act as a three-dimensional grating and produce diffraction.
- The diffraction pattern contains complete information on the placement of scatterers
(electrons in atoms, not nuclei).
- By Fourier transforming the diffraction pattern, we can obtain information on the structure
of the molecule in the crystals.
Experimental details:
- Solubilization of the over-expressed protein.
- Obtaining crystals that diffract.
- Structure determination by diffraction of protein crystals.
- Size of a molecule: no theoretical limit.
LECTURES SUMMARY
Doorslaer, R.F.J.F. Van
TU EINDHOVEN BMT | 23-04-2018
,TABLE OF CONTENTS
College 1: 23-04-2018 ...................................................................................... 3
tentamen........................................................................................................ 3
Structural biology ................................................................................................ 3
Intrinsically disordered proteins ............................................................................ 3
X-ray and nmr .................................................................................................. 3
protein structure elucidation ................................................................................... 3
x-ray crystallography .......................................................................................... 3
nuclear magnetic resonance (nmr) ......................................................................... 4
proteins ......................................................................................................... 4
Protein crystallization ........................................................................................ 4
case study: control of epigenetics by bromodomain inhibitors ........................................... 5
College 2: 23-04-2018 ...................................................................................... 7
proteins ............................................................................................................ 7
Protein domains................................................................................................ 7
College 3: 30-04-2018 .................................................................................... 10
Signal transduction 1 .......................................................................................... 10
Receptor tyrosine kinases (RTK) .......................................................................... 10
chemical induced dimerization ............................................................................ 11
College 4: 02-05-2018 .................................................................................... 14
Signal transduction 2 .......................................................................................... 14
Receptor tyrosine kinases .................................................................................. 14
g protein coupled receptors ............................................................................... 15
College 5: 07-05-2018 .................................................................................... 18
enzymes and protein profiling (abpp) ....................................................................... 18
College 6: 14-05-2018 .................................................................................... 21
labeling of proteins, assays and hts ......................................................................... 21
College 7: 17-05-2018 .................................................................................... 24
dna: synthesis, sequencing, therapy (h3) .................................................................. 24
College 8: 24-05-2018 .................................................................................... 26
14-3-3 protein-protein interaction .......................................................................... 26
College 9: 28-05-2018 .................................................................................... 27
Protein engineering ............................................................................................ 27
Rational approach ........................................................................................... 27
combinational approach .................................................................................... 27
evolution ...................................................................................................... 28
College 10: 31-05-2018 ................................................................................. 29
, microfluidics .................................................................................................... 29
College 12: 07-06-2018 ................................................................................. 31
Clinical chemistry .............................................................................................. 31
lung cancer & liquid biopsy ................................................................................ 31
College 13: 11-06-2018 ................................................................................. 32
Chemical synthesis of peptides chapter 5 .................................................................. 32
Amino acid nomenclature and properties ............................................................... 32
amide coupling reagents and peptide synthesis ........................................................ 32
spss............................................................................................................. 33
guided selfstudies ................................................................................................. 34
‘100 years of crystallography’ ................................................................................ 34
Phospho-Ser/Thr-binding domains ........................................................................... 36
‘Chemical Induced Dimerization’ ............................................................................ 38
“Small-molecule inhibitors of the interaction between TNF and TNFR“ .............................. 40
‘Enzymes, Kinases, Proteases, Activity-Based Protein Profiling’ ....................................... 42
Fluorophores, Protein Labeling, HTS ........................................................................ 44
“DNA” ............................................................................................................ 46
“Chemical Biology of 14-3-3 proteins” ...................................................................... 47
“peptide synthesis” ............................................................................................ 49
, COLLEGE 1: 23-04-2018
- Chemical Biology is the manipulation of biological systems.
- Gene lockouts are black and white switches, they either are active or not, RNAi is used to
control this.
TENTAMEN
- Learn Nobel prizes.
- Learn amino acids with their characteristic groups identify those in electron cloud
image.
- Rigidity: what are the most important factors in rigidity as anchoring principle/interaction
with protein pockets?
STRUCTURAL BIOLOGY
INTRINSICALLY DISORDERED PROTEINS
These proteins are incorrectly folded and measure up to 30-40% of the total amount of proteins
present in our bodies. They cause 60-70% of all diseases and are therefore important to target with
medicines. They do not have nicely folded 3D structures as normal proteins but their structure
fluctuates. What is special, is that their function depends on this fluctuation in structure.
IDP’s do not have binding pockets and can take on toxic forms.
An important example is the drug for Alzheimer’s disease: Tau. This protein is very difficult to
target by reasons stated above and is therefore hard to treat when Tau takes on a dangerous
structure to the brain.
X-RAY AND NMR
- CD, Fluorescence spectroscopy and Mass spectroscopy are also used, however, X-ray and
NMR are the most common.
PROTEIN STRUCTURE ELUCIDATION
X-RAY CRYSTALLOGRAPHY
Principles:
- Crystals act as a three-dimensional grating and produce diffraction.
- The diffraction pattern contains complete information on the placement of scatterers
(electrons in atoms, not nuclei).
- By Fourier transforming the diffraction pattern, we can obtain information on the structure
of the molecule in the crystals.
Experimental details:
- Solubilization of the over-expressed protein.
- Obtaining crystals that diffract.
- Structure determination by diffraction of protein crystals.
- Size of a molecule: no theoretical limit.
