Table 1.

Protein structures

Structure Description Detection Method Image

Name
Primary Sequence of amino From DNA by translating the
acids connected with codons into Amino Acids.
peptide bond Terminus identified after
cleavage and electrophoresis.

Secondary Pattern of folding 1. Bioinformatics numerically

involving peptide predict structure based on 1
chain backbone structure. e.g. Ali2D,
HHomp, Quick2D
2. FTIR/DSC/CD for
conformational changes in 2
structure

Tertiary 3D shape of protein X-ray crystallography, NMR,

from folding of a Dual Polarization
single polypeptide interferometry, CD, Cryo EM,
chain SAXS, SANS, Homology
Modeling

Quaternary 3D shape from 3 methods with SDS page, gel

interaction of multiple filtration, Western Blot
polypeptide chains

DNA/RNA
Table 2. Protein structure determination

Method Type Measured Sample Measurement

Quantity Type
X-ray X-ray 3-D molecular Pure protein Static (No
Crystallography structure crystals temperature
changes)
NMR Magnetic 3-D molecular Solution phase, Dynamic
Spectroscopy Field structure molecular size 5 to (Effects of
25 kDa unfolding due to
temperature
change)
Small Angle X- X-ray Volume, Solution phase, kDa Dynamic,
ray Scattering Molecular Mass, to GDa range quantitative
(SAXS) Folding State
Circular Polarized Secondary Solution Phase Protein
Dichroism (CD) light structure concentration,
Fraction of
secondary
structures
FTIR Infrared light Secondary Solution or solid Dynamic
structure phase qualitative
measurement of
conformational
change
DSC Calorimeter Changes in Solution or solid Dynamic,
enthalpy phase, nanogram to quantitative
associated with mg range measurement of
structer conformational
change
FRAP

FRET
Deep Nulling
Microscope

Analytical
Centrifuge
Table 3. Thermal active targeting
Application Area Method
Deep brain Iron Oxide NP coated with
stimulation membrane binding proteins
injected in vivo. HEK293
cells in vitro. Targeting
TPV1 Ca2+ channels.
Cancer 1. NP assisted targeting
(Neoplastic tissue 2. NP assisted drug release
growths) 3. NP assisted combined
targeting and drug release 5. GNR assisted delivery
4. NP tumor
preconditioning
Laser assisted 1. siRNA transfer by GNP
Photoporation laser heating
2. Delivery of Caspase 3
into mammalian cells
Tissue sealing 1. Sealing vessels for
laparoscopic surgery
2. Surgical resection and
organ removal
Hair follicle Manipulation of keratin by
removal and GNP synthesis in hair
dyeing follicles
Gene Spatial and temporal control
modification of GFP expression by RNAi
delivery
Tissue shrinkage
Effect Ref
Ca2+ concentration Chen et al.
increase in cells Neurotechniques
2015
expressing TRPV1 and
treated with MNP Huang et al.
Nature
Fluorescence change Nanotechnology
quantification of action 2015
potential detection
3. Size dependent NP Dreaden et al.
delivery to tumor BV Ther Deliv 2012
4.
Qin et al. CSR
2012
after targeting specific
receptor Park et al. PNAS
6. 2010
1. 80% reduction in GFP Heinemann et al.
expression PLOS ONE 2013
2. 53% reduction in cell
Heinemann et al.
viability with GNP Nanotech 2014
assisted laser heating
RF/Ultrasonic heating of Cezo et al. J Mech
tissue. Collagen/Elastin Behav Biomed
Mater 2014
denaturation at 60C to
100C is responsible for Reyes et al. Surg
seal strength. Endosc 2012
Hair used as nanoreactor Haveli et al. Nano
for NP synthesis by Lett 2012
HAuCl4 - dyeing of hair
Voght et al. J
Invest Derma
2006
Spatial control exhibited Braun et al. ACS
by blocking and Nano 2008
exposing part of laser
beam. Temporal control
by delayed application of
laser.
Neuromodulation

Cosmetics
Table 4. Nanoparticle assisted protein manipulation
Application Area Method
Neuromodulation GNP functionalized with
antibodies targeting Na+,
Ca2+, P2X3 receptor ion
channels in DRG neurons.
Patch clamped neurons used
with 532 nm CW laser.
Glioblastoma
Ablation
Laser assisted 1. siRNA transfer by GNP
Photoporation laser heating
2. Delivery of Caspase 3
into mammalian cells
Hair follicle Manipulation of keratin by
removal and GNP synthesis in hair
dyeing follicles
Gene Spatial and temporal control
manipulation of GFP expression by RNAi
delivery
Effect Ref
GNP directly modifies Carvalho-de-
membrane capacitance to Souza et al.
modulate electrical Neuron 2015
stimulation rather than
opening ion channels. Urban et al.
Nat Sci Rep
GNP heating allows 2016
regulation of current
across membrane
1. 80% reduction in GFP Heinemann et al.
expression PLOS ONE 2013
2. 53% reduction in cell
Heinemann et al.
viability with GNP Nanotech 2014
assisted laser heating
Hair used as nanoreactor Haveli et al. Nano
for NP synthesis by Lett 2012
HAuCl4 - dyeing of hair
Voght et al. J
Invest Derma
2006
Spatial control exhibited Braun et al. ACS
by blocking and Nano 2008
exposing part of laser
beam. Temporal control
by delayed application of
laser.
Table 5. Mechanisms of protein structural change
Energy modality Method Effect Ref
Heat

pH change

Heavy Metal
Salts

Detergents

Mechanical
Forces
 Table 5. Literature data on cellular protein denaturation
Target Instrument Rate End Onset Output Reference
Temp Temp
Ea ln{A}
(C) (C)
(kJ/mol)
AT-1 cells DSC 2C/min 70 41.4 0.5 159.7 52.20 HeABME2004
Suspensio 67.3 - 173.8 57.55
n 50 - 511.7 187.46
(HeABM 47.3 - 721.9 268.26
E2004) 5C/min 90 44.0 0.6 108.4 33.57
70 44.1 0.6 176.0 58.85
Untreated 50 - 746.5 276.11
FTIR 2C/min 70 40.3 0.2 141.5 45.67
Clonogenic 5C/min 52 - 633.2 232.97
assay
PI exclusion 5C/min 59 - 400.5 142.76
assay
AT-1 cells Calcein assay - 70 - 81.2 24.66 BhowmickJBME2
Attached 000
(HeABM PI exclusion - 70 - 245.2 86.29
E2004) assay
Clonogenic - 50 - 526.8 193.46
Untreated assay
AT-1 cells DSC (CP fit of 2C/min 70 40.27 128.6 41.0 QinABME201
HeABME2004 60 40.27 225.3 78.0 4
Untreated ) 50 40.27 382.4 139.0
HuH-7 DSC (CP fit of 2C/min 80.4 40.03 84.1 24.3 QinABME201
AravalliTCRT 70 40.03 114.5 35.9 4
Untreated 2012) 60 40.03 175.1 59.3
50 40.03 323.8 116.8
HDF cells FTIR 1C/min 80.54 42.53 119.8 37.0 QinABME201
70 42.53 148.7 47.8 4
Untreated 60 42.53 196.4 66.1
50 42.53 425.1 154.5
LNCaP FTIR 1C/min 83.52 40.88 61.4 15.3 QinABME201
cells 70 40.88 99.7 29.9 4
60 40.88 160.9 53.5
Untreated 50 40.88 472.7 169.0
LNCaP FTIR 2C/min 92 48 45.7 10 WolkersBBA2
cells 007
(PR (PR (PR
Untreated Calcul Calculate Calcul
ated) d) ated)
RBC FTIR 2C/min 90.92 - 51.95 11.275 WolkersSpectr
oscopy2010
Untreated
Platelets FTIR 2C/min 89.9 - 50.6 11.65 WolkersSpectr
oscopy2010
Untreated
 Table 6. Literature data on tissue protein denaturation

Target Instrument Rate End Onset Output Referenc

Temp Temp e
Ea ln{A}
(C) (C)
(kJ/mol)
Skin Pig Histology - 70 - 627.6 226.78 Henrique
sArchPat
h1947
Rat Birefringence - 90 - 306.3 104.09 Henrique
loss in collagen sArchPat
h1947
Coll Rat tail DSC 2C/min - 58.8 521 183.8 MilesJMB1
agen tendon 995

Rat tail Birefringence - - - 369.4 129.59 MaitlandLa

tendon loss serSurg199
7
Kangaro Shrinkage - - - 588.3 205.57 WeirJAmL
o CA1949
Tendon
Kidn Pork Histology - - - 256.94 88.68 HeIJH2004
ey (Thermal
necrosis)
Coll Rat tail FTIR 2C/min 80 573 142.1 44.90 Scheumann
agen tendon (PR (PR Thesis
2016
(Te 0N Calculate Calcul
mp pressure d) ated)
and Rat tail FTIR 2C/min 95 55 85 23.27( Scheumann
Pres tendon (PR PR Thesis
2016
sure) 2N Calculate Calcul
pressure d) ated)