Module 3

Question 1

Molecules “_______” or _______randomly

Answer 1

“tumble” or rotate

Question 2

Tc

Answer 2

rotational correlation time

Question 3

Three things that influence tumbling rates:

Answer 3

viscoscity

temperature

size of particle

Question 4

Molecular rotations cause ____ ___-_______ _____ , B loc(t)

Answer 4

local time-dependent fields

Question 5

NMR-active nuclei with \_\_\_\_\_ \_\_\_\_\_\_ \_\_\_\_\_\_can interact with other nuclei causing
spin relaxation (T1 and T2).

Answer 5

fluctuating local fields

Question 6

the __ and __ time constants describe the rate (T1= 1/R1) at which longitudinal and
transverse relaxation occur, respectively.

Answer 6

T1 and T2

Question 7

Where do molecular rotations occur from?

Answer 7

They occur from the influence of a single spin or many spins simultaneously

Question 8

What do molecular rotations depend on?

Answer 8

gama Bloc = omega knot

Question 9

Where does the fluctuation come from?

Answer 9

Random events ……
• Rotational diffusion
• Translational diffusion
• Vibrational / Librational motions
• Conformational sampling (conformational exchange)`

Question 10

The behavior of the random fluctuation can be described by a _______ function.

Answer 10

correlation

Question 11

Correlation function:

Answer 11

the measure of how quickly two variables change as a
function of time.

Or, how quickly the NH dipole (or other vector dipole) changes as a
function of time with respect to the external magnetic field (autocorrelation
function).

Question 12

The ______ ______ describes the distribution of motions (frequency of rotation) in a sample.

Answer 12

spectral density

Question 13

Tc is directly porportional to

Answer 13

MW

Question 14

T2 is inversely porportional to

Answer 14

MW

Question 15

Any particular source of a local magnetization field can be considered a _______ ______.

Answer 15

relaxation mechanism

Question 16

\_\_\_\_\_\_ mechanism (DD) :
influences of one local spin on another

Answer 16

Dipolar mechanism (DD)

Question 17

____ ___ ____ (CSA :

anisotropy of chemical shift tensor

Answer 17

Chemical shift anisotropy

Question 18

_____: non-symmetric electronic field (I>=1)

Answer 18

Quadropole

Question 19

DD > CSA > spin-rot

Answer 19

for 1/2 spin

Question 20

Quad.&raquo_space; DD > CSA > spin-rot

Answer 20

for spin > 1/2

Question 21

Since all these result from molecular rotations, this implies that there may be a degree of
\_\_\_\_\_\_\_ between mechanisms. Cross-correlation. TROSY-type experiments rely on
this phenomena (DD and CSA). TROSY  Transverse Optimized SpectroscopY

Answer 21

correlation

Question 22

In NMR, any source of a fluctuating nuclear interaction (global or local) can
lead to____ _____ (with respect to the external magnetic field).

Answer 22

spin relaxation

Question 23

A pattern or process of change, growth, or activity

Answer 23

Dynamics

Question 24

Molecules are not static!

Brownian motion……molecular tumbling

Internal motions ….. J-couplings, side-chain rotations

Fluorescence studies ….. quenching of aromatic residues within a protein

NMR ….. site-specific molecular dynamic information

Answer 24

Molecular Dynamics

Question 25

Internal motions …..

Answer 25

J-couplings, side-chain rotations

Question 26

Fluorescence studies …..

Answer 26

quenching of aromatic residues within a protein

Question 27

NMR …..

Answer 27

site-specific molecular dynamic information

Question 28

NMR Motional Timescale for Fast (ps-ns) ``` Motions: - - - NMR parameters - - ```

Answer 28

Flesibility Diffusion Domain motions ``` Spin relaxation (R1,R2, and hnNOE) Residual dipolar coupling averaging ```

Question 29

NMR Motional Timescale for Slow (us-ms) ``` Motions: - - - NMR parameters - - - - ```

Answer 29

Protein folding Enzyme catalysis Domain motions Line shape R1p dispersion Longitudinal magnetization exchange Hydrogen exchange Residual dipolar coupling averaging

Question 30

• Dipolar, CSA, Spin rotation, Quadropole (all result from a fluctuating Bloc) • Dipolar couplings are the origin of distance (NOE) and orientation (RDC) information and also provide a mechanism for transitions to occur that contribute to relaxation • Internal motions within a protein can be an additional source of relaxation in addition to overall tumbling

Answer 30

Mechanisms of spin relaxation

Question 31

• Keep track of random motions (rotations) [and Bloc(t)] • The FT of the auto-correlation function yields the spectral density function, J() • The spectral density function tells us about the probability of having a spin with the frequency appropriate to cause relaxation – this explains spin relaxation !! • Both T1 and T2 (and heteronuclear NOE) are proportional to the spectral density, J() (because of molecular tumbling)

Answer 31

The auto-correlation and spectral density functions

Question 32

``` Longitudinal elaxation (T1) (relaxation and local magnetic fields) ```

Answer 32

local fields are time dependent Bloc

Question 33

Due to molecular motions (rotations), ____-_________ _____ ___________ ________ ______ [Bloc(t), transverse components (x-y)] occur within the sample and interact with individual magnetic moments to rotate them into new positions– like an RF pulse! These transitions occur only at Bloc =  ◦

Answer 33

time-dependent local oscillating magnetic fields

Question 34

Bloc(t) fields vary in magnitude due to _____ __ _______ ____ ______ ________ _______ (orientations are relative to Bo). The spins are in “contact” with the thermal motions.

Answer 34

changes in orientation from random thermal motions

Question 35

For spins to "sense the Bloc(t) of another spin they must be?

Answer 35

very close to eachother

Question 36

Since these local fields effect the orientation of individual magnetic moments, both the magnitude and orientation of the ____ _________ can be affected leading to spin relaxation and re-establishment of equilibrium magnetization along the z-axis.

Answer 36

BULK magnetization

Question 37

lattice is also known as

Answer 37

reservoir of energy = molecular motion

Question 38

longitudinal relaxation is also known as

Answer 38

spin-lattice relaxation (T1)

Question 39

Transverse or spin-spin relaxation (time constant  T2) | - loss of phase coherence of the ____ ____ in the transverse plane (xy-plane)

Answer 39

nuclear dipoles