A new paradigm of protein structural organization · 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

Nekrasov A.N., Anashkina A.A., Zinchenko A.A. Moscow, Russia

A new paradigm of protein

structural organization

Presenter

Presentation Notes

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


POSITION SHANNON’S ENTROPY

BASE 1 BASE 2 BASE 3


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


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


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)


123 123

177

224

177

123

100

200

100

200

100

200

PROTECTIVE ACTIVITIES of hPrxVI, hPrxVI∆178 & hPrxVI∆124


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


PROTEIN SITES CLASSIFICATION BY THE DENSITY OF FIRST RANK ELIS

TOPOLOGICALLY CONSTRAINED SITE

ADD+

ADD- TOPOLOGICALLY VARIABLE SITE

NORMAL TOPOLOGICALLY STANDARD SITE


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

[email protected]

[email protected]

ОСОБЕННОСТИ ОРГАНИЗАЦИИ

ИНТЕРФЕЙСОВ

ВЗАИМОДЕЙСТВИЯ

В БЕЛОК-БЕЛКОВЫХ

КОМПЛЕКСАХ

SPATIAL STRUCTURES OF ENZYME-INHIBITOR COMPLEXES


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


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

Documents

A new paradigm of protein structural organization · 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