Post on 21-Aug-2020
Nekrasov A.N., Anashkina A.A., Zinchenko A.A. Moscow, Russia
A new paradigm of protein
structural organization
Proteins: structure and function
– Enzymes – Structural – Transport – Motor – Storage – Signaling – Receptors – Gene regulation
"THE SPATIAL STRUCTURE AND FUNCTIONAL PROPERTIES OF PROTEINS ARE COMPLETELY CODED IN THEIR SEQUENCE" (Anfinsen, 1961)
?
Linus Pauling
Protein structures >90 000
Protein sequences >20 000 000
Experimental Data
Anfinsen, B. C., Haber, E., Sela, M., and White, Jr, F. H. "The kinetics of formation of native ribonuclease during
oxidation of the reduced polypeptide chain". Biochemistry, (1961) v. 47, pp.1309-1314
“… the information for the …. assumption of the native secondary and tertiary structures, is contained in the amino acid sequence itself.”
VS
“...proteins are slightly corrected random heteropolymers” Ptitsin O.B., Vol‘kenshtein M.V. J.Biomol. Struct. Dyn. (1986) v.4(1), pp.137-156
DATABASE NRDB (release 3.0) NRDB (release 6.0) NRDB (release 9.0)
PROTEINS 192519 252926 534938
J Biomol Struct Dyn. v. 20, p. 84
DATA FOR THE ANALYSIS
METHOD OF PROTEIN SEQUENCE ANALYSIS
S = - P log PΣ Σ 2i, j i, j
k k k 20
i=1,20 j=1,20
20
n n+k-2 n+k-1 n+k
A
C
DE
WY
A
C
DE
WY
A
C
DE
WY
A
C
DE
WY
A
C
DE
WWY
A
C
DE
WY
A
C
DE
WY
A
C
DE
WY
k = {0,1,2,… 50} n = {1,2,3,…L}
L
k
P k-2 P P P
k-1 k k+1
n+k 1 +
...
...
...
...
...
...
...
...
{ { ACDE...WY
{ { ACDE...WY
{ { ACDE...WY
{ { ACDE...WY
{ { ACDE...WY
J Biomol Struct Dyn. v. 20, p. 84
POSITION SHANNON’S ENTROPY
BASE 1 BASE 2 BASE 3
J Biomol Struct Dyn. v. 20, p. 84
S0SK/ X 105
K
1.0012
1.0010
1.0008
1.0006
1.0004
1.0002
1.0
0 5 10 15 20 25 30 35 40
REPRESENTATION OF SEQUENCE AS A SET OF INFORMATIONAL UNITS
{ε = 2δ + 1
INFORMATIONAL UNITS
AMINO ACID RESIDUES
COMPUTATION OF INFORMATIONAL UNITS POPULATION PROFILE OF PROTEINS
IU EQUIVALENCE
IU-DATABASE
AMINO ACID RESIDUES
INFORMATIONAL UNITS
GAUSSIAN APPROXIMATION OF POPULATION PROFILE OF PROTEINS
AMINO ACID RESIDUES
ρ1
ρ2>ρ1
GRAPHICAL PRESENTATION OF PROTEIN INFORMATIONAL STRUCTURE
ρ/2
L (sequence)
1AC5A 1BJWA
1AO5A C N
ANIS – ANalysis of Informational Structure method
SEQUENCE
ρ/2
ELIS - High Rank ELements of Informational Structure
J Biomol Struct Dyn. v. 21 , p. 61 5
C N
C N
ρ/2
HIGH RANK ELIS RELATIONS WITH RESPECT TO STRUCTURAL DOMAINS
Pepsin (1AM5.PDB)
T-Lymphocyte Adhesion Glycoprotein(1HNG-A.PDB)
Myosin Regulatory Domain (1SCM-C.PDB)
C N
ρ/2
C N
ρ/2
C N
ρ/2
γ-CRYSTALLIN (1GCR.PDB)
10 20 30 40 50 60 70 80
10
20
30
40
50
60
70
80
90
100
110
120
130
140
150
160
170
W157
W68
Y16
M90
HIGH RANK ELIS RELATIONS WITH RESPECT TO STRUCTURAL DOMAINS
CATALYTIC SITES IDENTIFICATION METHOD
NAA
ρ/2
TRYPSIN FROM BOS TAURUS (EC: 3.4.21.4) 1CO7.PDB
10 20 3 0 40 50 6 0 70 80 9 0 100 1 10
10
20
30
40
50
60
70
80
90
100
110
120
130
140
150
160
170
180
190
200
210
220
230
240
H57
D102
S195
NAA
ρ/2
J Biomol Struct Dyn. (2008) v. 25, p. 554
PEPSIN FROM GADUS MORHUA (EC: 3.4.23.1) 1AM5.PDB
2 10 18 26 34 42 50 58 66 74 82 90 98 106 114 122 130 138 146 5
10
20
30
40
50
60
70
80
90
100110120
130
140
150160
170
180
190
200
210
220
230
240
250260270
280
290
300310
320
G177
D32
D215
1 4 162 170 178
NAA
ρ/2
J Biomol Struct Dyn. (2008) v. 25, p. 554
RNAse A FROM BOS TAURUS (EC: 3.1.27.5) 1AQP.PDB
10 20 30 40
10
20
30
40
50
60
70
80
90
100
110
120
H12
K41
H119
NAA
ρ/2
J Biomol Struct Dyn. (2008) v. 25, p. 554
ACTIVE CENTRE OF HEMOGLOBIN β-CHAIN
Paoli et. al. JMB (1 996) v. 256, p. 775
HIGH RANK ELIS OF HEMOGLOBIN β-CHAIN (1BZ0.PDB)
2 6 10 14 18 22 26 30 34 38
10
20
30
40
50
60
70
80
90
00
110
120
130
140
40 42 44 46 48 50 52 54
1
H87
H58
CYTOCHROME C
(1HRC.PDB)
HEMOGLOBIN
(1BZO.PDB)
10 20 30 40 50
10
20
30
40
50
60
70
80
90
100
H18
M80
HIGH RANK ELIS OF CYTOCHROME C FROM EQUUS CABALLUS (1RHC.PDB)
NAA
ρ/2
1020
3040
5060
70
10 20 30 40 50 60 70 80 90
100
110
120
130
140
150
160
170
180
190
200
210
220
230
240
250
260
270
>PROTEIN SEQUENCE AQTVPYGIPL IKADKVQAQG FKGANVKVAV LDTGIQASHP DLNVVGGASF VAGEAYNTDG NGHGTHVAGT VAALDNTTGV LGVAPSVSLY AVKVLNSSGS GSYSGIVSGI EWATTNGMDV INMSLGGASG STAMKQAVDN AYARGVVVVA AAGNSGNSGS TNTIGYPAKY DSVIAVGAVD SNSNRASFSS VGAELEVMAP GAGVYSTYPT NTYATLNGTS MASPHVAGAA ALILSKHPNL SASQVRNRLS STATYLGSSF YYGKGLINVE AAAQ*
>PROTEIN SEQUENCE
*
AQTVPYGIPL IKADKVQAQG FKGANVKVAV LDTGIQASHP DLNVVGGASF VAGEAYNTDG NGHGTHVAGT VAALDNTTGV LGVAPSVSLY AVKVLNSSGS GSYSGIVSGI EWATTNGMDV INMSLGGASG STAMKQAVDN AYARGVVVVA AAGNSGNSGS TNTIGYPAKY DSVIAVGAVD SNSNRASFSS VGAELEVMAP GAGVYSTYPT NTYATLNGTS MASPHVAGAA ALILSKHPNL SASQVRNRLS STATYLGSSF YYGKGLINVE AAAQ
>PROTEIN SEQUENCE
*
AQTVPYGIPL IKADKVQAQG FKGANVKVAV LDTGIQASHP DLNVVGGASF VAGTNGMDVI NMSLGGASGS TAMKQAVDNA YARGVVVVAA AGNSGNSGST NTIGYPAKYD SVIAVGAVDS NSNRASFSSV GAELEVMAPG AGVYSTYPTN TYATLNGTSM ASPHVAGAAA LILSKHPNLS ASQVRNRLSS TATYLGSSFY YGKGLINVEA AAQ
METHOD OF NEW RECOMBINANT PROTEIN DESIGN
J Biomol Struct Dyn. v. 24(5), p. 455
TRUNCATED FORMS OF HUMAN 1-CYS PYROXIREDOXIN (PrxVI)
J Biomol Struct Dyn. v. 24, p. 455
123 123
177
224
177
123
100
200
100
200
100
200
PROTECTIVE ACTIVITIES of hPrxVI, hPrxVI∆178 & hPrxVI∆124
J Biomol Struct Dyn. v. 24, p. 455
TRUNCATED FORMS OF INTERLEUKIN IL-13
Biochemistry (Moscow), (2009) vol. 74, p. 493
W34Y43
C70
100 100 100
A
B
C
D
SPATIAL STRUCTURE OF TUMOUR NECROSIS FACTOR (TNF)
Bioorg Khim. (201 0) vol. 36, p. 327 (RUS)
INFORMATIONAL STRUCTURE OF TNF
Bioorg Khim. (201 0) vol. 36, p. 327 (RUS)
W28
W114
S86
100100
TNF ELIS FRAGMENTS
STRUCTURE FORMING
AND STRUCTURE STABILAZING
PENTAPEPTIDES
Protein Informational Profile
PHEROMONE ER-1
(2ERD.PDB)
ρ/2
SEQ
UEN
CE
J Biomol Struct Dyn. vol. 28(1 ), p. 85.
5 10 15
Y29
E23
S17
E12
A6
S34
C
N
BARNASE (1BGS.PDB)
CONFORMATIONS OF LARGEST CLUSTERS OF FIRST RANK ELIS AFTER MD
EIKFL 65% EQLGR 82% EVASN 65% HLLAQ 44%
KFLEQ 33% KNLLL 41% ILAAA 47%
LDEQL 69% QNLLI 43% NETMA 45%
QQLEI 40%
DISTRIBUTION OF FIRST RANK ELIS DISTANCE
ADD - Anomal Distribution Density
Normal Distribution Density (R~RHLCD)
1.6 x106
1.4 x106
1.2 x106
1.0 x106
0.8 x106
0.6 x106
0.4 x106
0.2 x106
2 4 6 8 10 12 14 16 18 20 22 24
0
R
N
J Biomol Struct Dyn. vol. 28(1 ), p. 85.
PROTEIN SITES CLASSIFICATION BY THE DENSITY OF FIRST RANK ELIS
TOPOLOGICALLY CONSTRAINED SITE
ADD+
ADD- TOPOLOGICALLY VARIABLE SITE
NORMAL TOPOLOGICALLY STANDARD SITE
J Biomol Struct Dyn. vol. 28(1 ), p. 85.
ADAPTABLE CONFORMATIONAL CHANGES WHILE POLYPEPTIDE CHAINS INTERACTION
E
R
1
2
1A
1B
2A 2B
3A 3B
AB
3
AAB
B
FACTORS THAT INFLUENCE ON INTERACTION BETWEEN
POLYPEPTIDE CHAINS
- EXISTENCE OF FUNCTIONAL GROUPS OF AMINO ACID RESIDUES THAT PROVIDE INTERACTION
- ABILITY OF POLYPEPTIDE CHAIN TO CHANGE CONFORMATION IN ORDER TO PROVIDE OPTIMUM DISTANCE FOR INTERACTING FUNCTIONAL GROUPS
Conclusions 1. Proposed and statistically justified a new paradigm
of the structural organization of proteins, according to which the basic element of a naturally occurring amino acid sequence if information unit.
2. On the basis of the paradigm developed a method of information structure analysis (ANIS) of proteins. The method allows to reveal hierarchically organized structural elements of the informational structure (ELIS) in the amino acid sequences.
3. Demonstrated examples of the ANIS method applications to explain the mechanism of proteins function. In works on protein engineering the method was used for the design of amino acid sequences with modified physico-chemical and functional characteristics, but retains the ability to self-organize.
Acknowledgements
This work was partially supported by grant 12-04-01776-а of Russian Foundation for Basic Research
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Alexei N. Nekrasov (ANIS method, IU,
ELIS, TNF, IL-13, PrxVI)
Alexei A. Zinchenko (IU, IS, ELIS)
Lada E. Petrovskaya (IL-13, TNF)
Sergey I. Rogov (IU)
Vitaly V. Radchenko (PrxVI)
Tatiana M. Shuvaeva (PrxVI)
Ljudmila N. Shingarova (IL-13, TNF)
Institute of Cell Biophysics RAS Pushchino Vladimir I. Novoselov (PrxVI)
Eugenyi E. Fesenko
Valery M. Lipkin
Mikhail P. Kirpichnikov
Steklov Mathematical Institute RAS Moscow Igor V. Volovich Sergey V. Kozyrev (ANIS method)
AUTHORS
Engelhardt Institute of Molecular Biology RAS, Moscow Anastasia A. Anashkina (IU, ELIS)
THANKS FOR YOUR
ATTENTION
alexei_nekrasov@mail.ru
anastasya.anashkina@gmail.com
ОСОБЕННОСТИ ОРГАНИЗАЦИИ
ИНТЕРФЕЙСОВ
ВЗАИМОДЕЙСТВИЯ
В БЕЛОК-БЕЛКОВЫХ
КОМПЛЕКСАХ
SPATIAL STRUCTURES OF ENZYME-INHIBITOR COMPLEXES
J Biomol Struct Dyn. vol. 28(1 ), p. 85.
TRPS/BPTI SUBT/CI2A PME/PMEI RNAse/RI PPE/aPI MMP3/TIMP
ADD-/
/ADD-
/ADD-ADD-
/NORM
/ADD+
/ADD+
93.6
1.6
0.0 95.2
39.0
0.0
33.7 72.7
33.8
21.1
31.0
31.4
41.2
23.5
14.3
14.3
64.3
9.6
6.3
46.9
0.0
1.6
3.2 4.8
11.7
2.6
13.0 27.3
5.6
0.0
8.5 14.1
0.0
0.0
3.9 3.9
0.0
0.0
7.1 7.1
24.6
0.0
12.6 37.2 15.8
84.2
TYPE CONTACT
/ADD+
/NORM
/
/NORM
/NORM
/ADD+
93.6
1.6
0.0
39.0
0.0
33.7
33.8
21.1
31.0 85.9
31.4
41.2
96.1
14.3
14.3 92.9
64.3
9.6
6.3
62.8
0.0
1.6
3.2 4.8
11.7
2.6
13.0
5.6
0.0
8.5
0.0
0.0
3.9 3.9
0.0
0.0
7.1 7.1
24.6
0.0
12.6 15.8
84.2
IS TYPE CONTACTS REALIZED IN HYDROLASE-INGIBITOR COMPLEXES
J Biomol Struct Dyn. vol. 28(1 ), p. 85.
INTERLEUKIN-2 (IL-2) & RECEPTOR COMPLEX (2B5I.PDB)
γ-chain β-chain
α-chain
IL-2
VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY (1BJ1.PDB)
МЕТОД ПОЛУЧЕНИЯ РЕКОМБИНАНТНЫХ
ВАКЦИН
CREATION OF RECOMBINANT VACCINE
Vaccine v. 26, p. 2688
P1 protein from Saccharomyces cerevsiae
ADD+ site
Virus-like particle
FVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
Beta- chain C-peptide Alpha-chain
PROINSULINE INFORMATIONAL STRUCTURE
DIRECTIONS OF POSSIBLE COLLABORATION
1. Development of tools for protein design and engineering tools.
2. Development of a method of hierarchical protein folding. 3. Computer modeling of spatial structure and investigate
forming rules of protein subunits. 4. Design and modification of pharmacologically important
proteins. 5. Research of protein structure organization and
mechanisms of enzymes activity. 6. "Molecular tweezers“ by fibronectin
Classic view: levels of structural organization of proteins
sequence secondary structure
tertiary structure
quaternary structure
A
B
C
D
Biochemistry (Moscow), (2009) vol. 74, p. 493