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Structural Bioinformatics Flashcards

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1
Q

oldest method of how protein structures are determined

A

X-ray crystallography

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2
Q

small protein crystals are exposed to intense x-ray beams

A

X-ray crystallography

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3
Q

The xray in xray crystallography are scattered (diffracted) by the protein crystals

A

Xray crystallography

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4
Q

In X-ray crystallography, it is used to calculate an electron density map of all the heavy atoms

A

positions of the diffraction spots
intensity

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5
Q

X ray crystallography

crystallographers determine the x,y,z coordinates of all the atoms using the _ of the protein

A

known sequence

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6
Q

Give an advantage of X-ray crystallography

A

permits the determination of very large macromolecular structure

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7
Q

What are the disadvantages of Xray crystallography?

A

computationally difficult
experimentally challenging
protein does not resemble the normal physiological state

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8
Q

What is the first protein structure resolved by xray crystallography?

A

Myoglobin

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9
Q

allows one to study structure and dynamics of molecules in a liquid state or in a near-physiological environment

A

NMR spectroscopy

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10
Q

What does NMR mean?

A

Nuclear magnetic resonance

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11
Q

protein structure is determined by measuring how radio waves are absorbed by atomic nuclei such as hydrogen (1H), isotopically labeled carbon (13C), or nitrogen (15N)

A

NMR spectroscopy

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12
Q

absorption measurement allows one to determine how much nuclear magnetism is transferred from one atom (or nucleus) to another

A

NMR spectroscopy

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13
Q

In NMR spectroscopy, _ is used to determine how much nuclear magnetism is transferred from one atom (or nucleus) to another

A

absorption measurement

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14
Q

is determined for as many protein atoms as possible using complex multi-dimensional NMR experiments

A

Magnetic transfer

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15
Q

a computer will analyze the distance geometry or simulated annealing from each NMR experiment

A

NMR spectroscopy

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16
Q

probably more reflective of the true solution behavior of proteins as most proteins seem to exist in an ensemble of slightly different configuration

A

Blurrogram structures

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17
Q

What does RMSD mean

A

Root mean square deviation

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18
Q

indicative of a good structure

A

RMSD of <1A

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19
Q

typical of a poorly determined structure

A

> 2A

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20
Q

What is the advantage of NMR spectroscopy?

A

experimentally simpler than xray crystallography
NMR structures more likely resemble those seen in the normal physiological environment of the cell

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21
Q

direct visualization technique

A

Cryo-EM

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22
Q

True or False: The quality of an NMR structure determination effort is typically given by how close these superimposed structures may be (blurrogram structures)

A

True

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23
Q

What are the disadvantages of NMR spectroscopy?

A

limited by the size of the molecule being studied (smaller proteins are preferred) and the solubility of the molecule (membrane proteins cannot be studied)
requirement for special isotopically labelled molecules (expensive)
inherently less precise than X-ray structures

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24
Q

protein samples are quickly frozen in water (creating vitreous ice) and then placed under powerful electron beams with electron walengths of 1-2A

A

Cryogenic Electron Microscopy

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25
What is the electron wavelength used for Cryo-EM?
1-2A
26
What are the advantages of using Cryo-EM?
cryo-EM sample preparation is much easier cryo-EM structures likely resembles those seen in the normal liquid environment of the cell
27
What are the disadvantages of Cryo-EM?
limited by the size of the molecule being studied (larger proteins are preferred)
28
What are the different types of protein structural studies?
Single crystal X-ray Diffraction (SC-XRD) Nuclear Magnetic Resonance (NMR) Cryo-genic Electron Microscopy
29
What are the hierarchal method of proteins?
Primary Secondary Tertiary Quaternary
30
amino acid sequence form
primary structure
31
The chain cannot exist in an extended string due to chemical nature and steric restrictions of side chains; needs to fold
primary structure
32
What are the five classes of Secondary structure?
alpha helices beta-pleated sheets (less abundant) beta turns omega loops 3/10 helices
33
globular and membrane proteins
tertiary structure
34
assemblage of tertiary structure
Quaternary structure
35
worldwide central repository of structural information of biological macromolecules
Protein DataBank
36
Who manages PDB?
Research Collaboratory for Structural Bioinformatics
37
interface of PDB
structure explorer
38
allows the user to read the summary information of a protein structure, view and download structure coordinate files, search for structure neighbors of a particular protein or access related research papers through links to the NCBI PubMed database
Protein Databank
39
four characters of either letters A to Z or digits 0-9
PDBid
40
What are the PDB entries?
PDBid Title Authors Other information about entry Download and view button
41
42
When was the PDB data format created?
1907
43
PDB format is designed to be compatible with _
FORTRAN
44
What are the 2 parts of PDB data format?
header section atomic coordinate section
45
provides an overview of the protein and the quality of the structure
Header section
46
a specified number of columns with predetermined contents
Structure coordinate section
47
refers to protein atom information
ATOM
48
refers to atoms of cofactor or substrate molecules
HETATM
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What are the limitations of PDB format?
not designed for computer extraction of information from the records certain restrictions in the format have significantly complicated its current use maximum number of atoms per model: 99,999 maximum number of chains: 26
50
highly parable by computer software
mmCIF
51
What does mmCIF mean?
macromolecular crystallographic information file
52
developed by the NCBI to parse and sort pieces of information in PDB
MMDB
53
allow the information to be more easily integrated with GenBank and Medline through Entrez
MMDB
54
it includes bond connectivity information, for each molecule called chemical graph
MMDB
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What does MMDB mean?
molecular modeling database file
57
computer graphics program has been developed for visualizing and manipulating complicated 3-dimensional structures
Protein structural visualization
58
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allows users to visually manipulate the structural images through a graphical user interface
interactivity
60
a line drawing representing bonds between atoms
wire-frame diagram
61
the simplest form of model interpretation
wire-fram diagram
62
useful for localizing position of a specific residues in a protein structure or for displaying a skeletal form of a structure when Ca atoms of each residue are connected
Wire-frame diagram
63
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solid spheres and rods representing atoms and bonds respectively
Ball and sticks
64
can be used to represent the backbone of the structure
ball and sticks
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other term for Space-filing model
CPK model (Corey, Pauling, and Koltan)
67
each atom is described using large solid spheres with radii corresponding to the van der Waals radii of the atom
Space-filing model
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use cylinders or spiral ribbons to represent a-helices and broad, flat arrows to represent B-strands
Ribbon diagrams
69
allows easy identification of secondary elements
Ribbon diagram
70
gives a clear view of the overall topology of the structure
Ribbon diagrams

Bioinformatics (1 decks)

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