Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

DDD x > Week 4 Part 1 > Flashcards

Week 4 Part 1 Flashcards

1
Q

What is structural biology?

A

A branch of molecular biology, biochemistry and biophysics concerned with the molecular structure of biological marcomolecule, how they acquire the structure they have, and how alteration in their structure affect their functions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Where does structural biology fit in?

A
  1. Research and development stage

2. Very early on, when a target is determined

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

How long does it take to bring a drug to market?

A

~15 years

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the average cost to bring a drug to market?

A

~$800 million

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Why are new approached and methods for drug discovery being employed?

A

Reduce time

Expense of bringing a drug to market

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Why is structural biology important?

A
  1. Try to understand 3D structure
  2. Understand in terms of function/inhibition
  3. By determining their atomic structure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the different experimental approaches for structural biology?

A
  1. X-ray crystallography
  2. NMR
  3. Cryo-electron microscopy
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are the computational approaches to structural biology?

A
  1. Homology modelling
  2. Ab initio modelling
  3. Molecular docking
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is Homology modelling?

A

Modelling a protein 3D structure using a known experimental structure of a homologous protein (the template)

Provides “low-resolution” structure - sufficient information about spatial arrangement of important residues in the protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is Ab initio modelling?

A

These methods attempt to identify structure with minimum free energy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the molecular docking?

A
  1. Model the interaction between a small molecule and a protein at the atomic level - characterise behaviour of small molecules in the binding side of target proteins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What are the 2 predictions of molecular docking?

A
  1. Prediction of the ligand conformation as well as its position and orientation within these sites
  2. Assessment of the binding affinity
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the aim of molecular docking?

A

Give a prediction of the ligand-receptor complex structure using computation methods

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How can molecular docking be achieved,

A
  1. Sampling confirmations of the ligand in the active site of the protein
  2. Ranking these confirmations via a scoring function
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is virtual screening?

A

Computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is De-novo design?

A

The three-dimensional structure of the receptor is used to design newer molecules

It involves structure determination of lead target complexes and the design of lead modifications using molecular modelling tools

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What can de novo design be used to design?

A

New chemical classes of compound that present similar substituents to target using a template or scaffold

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is fragment-based drug discovery?

A

Identify small chemical fragments
Bind only weakly to biological target
Growing/combining them to produce a lead with higher affinity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is protein-ligand models?

A

Predict the position and orientation of a ligand (or a small molecule) when it is bound to a protein receptor or enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

How can structural biology experiment guide lead identification and optimisation?

A
  1. Virtual screening
  2. De-Novo design
  3. Fragment-based drug discovery
  4. Protein-ligand models
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

For any experimental technique, what do we have to do?

A

Purify the protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Where can protein purification be isolated from?

A

Natural sources

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is a feature of protein purification?

A

Recombinant overexpression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What are examples of recombinant overexpression?

A
  1. E.coli
  2. Insect
  3. Human cells
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is the most common form of recombinant overexpression?

A

E.coli

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is a common technique for purification step?

A

Use affinity tags

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Why do you need a very homogenous sample of very pure protein?

A

Determine the structure of a single entity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

How do crystals form?

A

Local concentration of protein goes up

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

How does local concentration of protein go up?

A

Dehydration

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Why can we work with little small crystals now?

A

Have very bright beams which give us signal and resolution to achieve these structures

Have laser technique now

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What are the steps to X-day crystallography?

A
  1. Crystallisation
  2. Data collection
  3. Solving the structure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Crystallisation of X-Ray crystallography

A
  1. Increase the protein concentration in solution until it precipitated in an ordered fashion - form crystals
  2. Crystals take from a few hours to weeks/months to grow
  3. 10mg/ml protein concentration and no molecular weight limitations
  4. can either be “co-crystallised” or “soaked” into existing crystals
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What does the size and quality of crystal depend on?

A
  1. Exact details of the solvent
  2. Procedure used

Procedures must be optimised

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Why are smaller crystals much more common now?

A

Advances in data collection methods

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Data collection of X-ray crystallography?

A
  1. Crystals are placed in an X-ray beam and diffraction is observed
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is diffraction due to?

A

Interaction between radiation and the regular microscopic arrangement of molecules in the crystals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What does the angle of deflection depend on?

A
  1. Structure of the crystal
  2. Orientation relative to beam
  3. Wavelength of radiation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What can having a regular pattern of proteins in regular array tell?

A

That they diffract in the same manner
They all become additive
Get a diffraction pattern in terms of intensity and spacing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What makes use of data collected at synchrotrons?

A

90% of macromolecule structures solved by X-Ray crystallography

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

What is a synchrotron light a source of?

A
  1. Different electron accelerator type
  2. Includes a storage ring in which desired electromagnetic radiation is generated
  3. Radiation is used in experimental stations located in different beam lines
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

What is a synchrotron?

A

Extremely powerful source of X-rays

X-rays are produced by high energy electrons as they circulate around the synchrotron

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

What does a synchrotron machine exist to do?

A

Accelerate electrons to extremely high energy and then make them change direction periodically

Resulting X-rays are emitted as dozens of thin beams, each directed toward a beamline best to the accelerator

43
Q

What do you get with a synchrotron?

A

Very high large single wavelength of monochromatic X-rah beams that have very high intensity that generate very good signals

44
Q

What can diffraction pattern be used to generate?

A

Map of electron density within the crystal

45
Q

What can be built into the map of electron density?

A
  1. Atoms and molecules
46
Q

What can the electron density nap be used to reconstruct?

A
  1. Molecular structure

2. X,Y,Z coordinates of the atoms - tells you the position of atoms in the protein

47
Q

What does the final structure of the protein represent?

A
  1. The confirmation that was captured in the crystal lattice
  2. Single ‘frozen’ conformation
48
Q

What is crystallography now?

A
  1. High-throughout technique

2. Structure can be obtained within few days with well behaved data

49
Q

What is resolution?

A

How confidently we have resulted the distance between 2 atoms in the protein structure

50
Q

What does the diffraction pattern give?

A

The resolution of the data collected

51
Q

The higher the resolution

A

The smaller dots will be going outward

52
Q

The smaller the resolution

A

The smaller dots keep coming in

53
Q

What does he final resolution of data depend on?

A
  1. How well you can refine the structure in confidence
  2. How good are the procedures to get 3D structure
  3. Model building
54
Q

What depends on a specific resolution?

A

Determination of specific features of the structure

55
Q

What resolution is required to have a good definition of all secondary structure elements?

A

3.5 A and higher

56
Q

Resolution less than 2.5-3.0 A and higher

A
  1. Details of the side chain conformation

2. Orientation of the peptide planes

57
Q

What can NMR data be used to determine?

A

Structure of biomolecule in solution

No crystals are required

58
Q

What does NMR measure?

A

The transition between energy levels of nuclei with a nuclear magnetic moment in external magnetic field

Study the nucleus rather than electrons

59
Q

What can be measured by NMR?

A

Only some isotopes for a given element have a nuclear magnetic moment different from 0

60
Q

What are the isotopes for biomolecules?

A 
1H
2H
13C
15N
19F
31P
61
Q

What are NMR application molecules?

A

Usually isotopicslly labelled

62
Q

How can you resolve NMR better?

A

The higher the separation of recorded data

63
Q

What is the consequence of protein becoming larger?

A

The peaks start broadening more
The separation is not good between the peaks
Resolving the structure in 3D becomes difficult

64
Q

What is the limitations to using NMR?

A
  1. Limited to ~25KDa did the size of the protein

2. Impurities

65
Q

Higher magnetic fields

A

Higher separation of recorded data

66
Q

What does NMR signal depend on?

A

It’s electronic environment

67
Q

Define chemical shifts

A

Measure differences between the frequency of the observed transition and the frequency of a reference standard

Measured in ppm

68
Q

What does each chemical shift correspond to?

A

NMR visible isotope in the protein

Can be assigned using 3D experiments

69
Q

What can chemical shift be used to reconstruct?

A

Secondary structure of a protein

70
Q

What can certain nuclei exchange?

A

Excitation energy when they are close together

Nuclear Oberhauser Effect (NOE)

71
Q

What is NOE?

A

Transfer of nuclear spin polarisation from one population of nuclear spins to another via cross-relaxation

72
Q

What can the strength of NOE signal be used to indicate?

A

Distance between nuclei-distance restraints

73
Q

If a structure cannot be determined

A

Functional data can still be derived

74
Q

What is NMR?

A

Quite sensitive technique

Record both weak intermediate and tight interactions using NMR

75
Q

Where is the protein-protein interaction?

A

Marco molar range

76
Q

Role of deuterium labelling?

A

Reduces the speed of decay of NMR signal but can be coupled with more labelling

77
Q

NMR spectra of proteins above ~25KDa

A

Become crowded
Signal become vastly reduced
Larger proteins - slower tumbling -broad lines

78
Q

What can signal be increased by?

A

TROSY techniques at high magnetic field

79
Q

TROSY experiment

A

Compensate for low sensitivity by using a high magnetic field strength

80
Q

What does 2H labelling reduce?

A

The speed of decay of the NMR signal
Many experiments can not be performed

Coupled with selective methyl labelling of residues

81
Q

Largest structure solved by NMR

A

Malate synthase G82 KdA

Not easy to determine

82
Q

Largest protein interaction study

A

GroEL/GroES complex

~900 kDa - more standard now

83
Q

Molecular docking

A

Class of computational methods used to fit or “dock” a molecule into its binding site

Can be manual or automatic

The interaction between molecule and target are calculated and used to rank the compounds

84
Q

What is molecular docking used in?

A

Structure-based virtual screening to identify molecules likely to bind to a given target

85
Q

What can automatic procedure used for?

A

Screen large numbers of compounds and avoid any bias

86
Q

Higher ranking molecules

A

More likely to bind to target

87
Q

What are the 3 majn types of docking approaches

A
  1. Rigid docking
  2. Flexible-ligand docking
  3. Flexible-protein docking
88
Q

Rigid docking

A

The structures of both the ligand and the target are treated as rigid bodies

Acceptable only if the active conformation of ligand is known or ligand is a rigid cyclic structure

89
Q

Flexible-ligand docking

A

The ligand is allowed to be flexible and different confirmations are explored

90
Q

Flexible-protein docking

A

Both the ligand and protein are allowed to be flexible

91
Q

Flexible-protein docking

A

Both the ligand and protein are allowed to be flexible

92
Q

What can some of lead compounds extracted from natural sources be used for?

A

Directly for medical applications

In many cases leads need to be further modified (low activity, High toxicity or serious side effects)

93
Q

What does lead tend to be?

A
  1. Smaller
  2. Less hydrophobic
  3. Less aromatic rings
  4. Less hydrogen bond acceptors
94
Q

Ligand efficiency

A

Binding affinity

Number of non-hydrogen atoms

95
Q

Ligand based

A

Screening based upon known Luganda of target

96
Q

Structure based

A

Find ligands that complement features of 3D structure of biological target

97
Q

Virtual screening: ligand based

A
  1. Uses known active molecules
  2. Identifies new ligands with similar properties - molecular shape, electrostatics
  3. Used virtual libraries of compounds
98
Q

Virtual screening: structure based

A
  1. Uses X-Ray or NMR 3D structure of the target protein
  2. Uses virtual libraries of compounds
  3. Compounds from library are docked in the target using a molecular docking
99
Q

If a lead cannot be discovered by screening

A

Designed from scratch

100
Q

De-novo design - ligand based

A
  1. Uses the structure of known ligands to build the pharmacoporic models
  2. More than one ligand is usually required
  3. Drugs can be designed in such a way that they fit the pharmacophoric model
101
Q

Pharmacophore

A

Summaries the important binding groups and their relative positions in space

102
Q

De-novo design - structure based

A
  1. Start with the 3D structure of target protein
  2. Rational design process to construct molecules complementary in binding
  3. Molecular modelling
103
Q

Protein and binding site

A
  1. A library of fragment is screened by NMR
  2. Binding of fragment A is detected
  3. Fragment A is optimised to increase interactions with target
  4. The fragment library is screened again in the presence of fragment A
  5. Binding of fragment B is detected
  6. Fragment B is optimised
  7. A linked is added to join 2 fragments
104
Q

Advantages of fragment linking approach

A
  1. The optimisation stage is faster
  2. It is more likely to find fragment binding sites than leads binding the whole bind site
  3. Different combinations of fragments can be tested (high level of diversity)

DDD x (17 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions