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Regularitati ascunse si corelatii in nano-bio-structuri
M. Popescu, A. Velea
NATIONAL INSTITUTE OF MATERIALS PHYSICS BUCHAREST-MAGURELE
Atomistilor Str. 105 bis, P.O. Box MG-7, 077125 Magurele-Ilfov, Romania
Phone: +40(0)21 3690185, Fax: +40(0)21 3690177, email: [email protected], http://www.infim.ro
Workshop Exploratoriu: "Nano Sisteme Dinamice: de la Concepte la Aplicatii Senzoristice" 22-23 septembrie 2010, Bucuresti
Cuprins
• Introducere
• Metode
• Colagen α1(I) uman
• Interferon β
• Concluzii
Introducere
Metode
• Pair correlation- Se calculeaza numarul de perechi de aminoacizi de acelasi fel situati la anumite
distante unul de celalalt- Se determina functia de corelare de perechi
• Fast Fourier Transform
00 0
1 1
( ) cos( ) sin( )2 n n
n n
AX t A n t B n t
0
/2
/2
1 1( ) ( ) ( )
2
Tin t
n n
T
G f A iB X t e dtT
0f n
0
2
T
Colagen α1(I) umanA 139
R 71
N 28
D 66
C 18
Q 49
E 75
G 391
H 9
I 24
L 48
K 57
M 13
F 27
P 278
S 60
T 45
W 6
Y 13
V 47
MFSFVDLRLLLLLAATALLTHGQEEGQVEGQDEDIPPITCVQNGLRYHDRDVWKPEPCRICVCDNGKVLCDDVICDETKNCPGAEVPEGECCPVCPDGSESPTDQETTGVEGPKGDTGPRGPRGPAGPPGRDGIPGQPGLPGPPGPPGPPGPPGLGGNFAPQLSYGYDEKSTGGISVPGPMGPSGPRGLPGPPGAPGPQGFQGPPGEPGEPGASGPMGPRGPPGPPGKNGDDGEAGKPGRPGERGPPGPQGARGLPGTAGLPGMKGHRGFSGLDGAKGDAGPAGPKGEPGSPGENGAPGQMGPRGLPGERGRPGAPGPAGARGNDGATGAAGPPGPTGPAGPPGFPGAVGAKGEAGPQGPRGSEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGAKGANGAPGIAGAPGFPGARGPSGPQGPGGPPGPKGNSGEPGAPGSKGDTGAKGEPGPVGVQGPPGPAGEEGKRGARGEPGPTGLPGPPGERGGPGSRGFPGADGVAGPKGPAGERGSPGPAGPKGSPGEAGRPGEAGLPGAKGLTGSPGSPGPDGKTGPPGPAGQDGRPGPPGPPGARGQAGVMGFPGPKGAAGEPGKAGERGVPGPPGAVGPAGKDGEAGAQGPPGPAGPAGERGEQGPAGSPGFQGLPGPAGPPGEAGKPGEQGVPGDLGAPGPSGARGERGFPGERGVQGPPGPAGPRGANGAPGNDGAKGDAGAPGAPGSQGAPGLQGMPGERGAAGLPGPKGDRGDAGPKGADGSPGKDGVRGLTGPIGPPGPAGAPGDKGESGPSGPAGPTGARGAPGDRGEPGPPGPAGFAGPPGADGQPGAKGEPGDAGAKGDAGPPGPAGPAGPPGPIGNVGAPGAKGARGSAGPPGATGFPGAAGRVGPPGPSGNAGPPGPPGPAGKEGGKGPRGETGPAGRPGEVGPPGPPGPAGEKGSPGADGPAGAPGTPGPQGIAGQRGVVGLPGQRGERGFPGLPGPSGEPGKQGPSGASGERGPPGPMGPPGLAGPPGESGREGAPGAEGSPGRDGSPGAKGDRGETGPAGPPGAPGAPGAPGPVGPAGKSGDRGETGPAGPTGPVGPVGARGPAGPQGPRGDKGETGEQGDRGIKGHRGFSGLQGPPGPPGSPGEQGPSGASGPAGPRGPPGSAGAPGKDGLNGLPGPIGPPGPRGRTGDAGPVGPPGPPGPPGPPGPPSAGFDFSFLPQPPQEKAHDGGRYYRADDANVVRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGESMTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQNITYHCKNSVAYMDQQTGNLKKALLLQGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKTSRLPIIDVAPLDVGAPDQEFGFDVGPVCFL
1464 aminoacizi
P02452 CO1A1_HUMAN
Colagen α1(I) uman
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Alanine
Chain Postion200 400 600 800 1000 1200 1400
0.0
0.2
0.4
0.6
0.8
1.0Arginine
Chain Position200 400 600 800 1000 1200 1400
0.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Aspartate
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Aspargine
B
Chain Position
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Cysteine
Chain Position
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Glutamate
Chain Position 200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Glutamine
Chain Position200 400 600 800 1000 1200 1400
0.0
0.2
0.4
0.6
0.8
1.0Glycine
Chain Position
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Histidine
Chain Position
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Isoleucine
Chain Position
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Leucine
Chain Position200 400 600 800 1000 1200 1400
0.0
0.2
0.4
0.6
0.8
1.0Lysine
Chain Position200 400 600 800 1000 1200 1400
0.0
0.2
0.4
0.6
0.8
1.0Methionine
Chain Position
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Phenyalanine
Chain Position200 400 600 800 1000 1200 1400
0.0
0.2
0.4
0.6
0.8
1.0Proline
Chain Position
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Serine
Chain Position
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Threonine
Chain Position200 400 600 800 1000 1200 1400
0.0
0.2
0.4
0.6
0.8
1.0Tryptophan
Chain Position200 400 600 800 1000 1200 1400
0.0
0.2
0.4
0.6
0.8
1.0Tyrosine
Chain Position
0 200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Valine
Pozitionari in lant:
Colagen α1(I) umanFFT:
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
-0.02
0.00
0.02
0.04
0.06
0.08
0.10
0.12 Alanine
Frequency
Am
plit
ud
e
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.01
0.00
0.01
0.02
0.03
0.04
0.05
0.06Arginine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.005
0.000
0.005
0.010
0.015
0.020
0.025
Aspargine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.01
0.00
0.01
0.02
0.03
0.04
0.05
Aspartate
Frequency
Am
plit
ud
e
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.005
0.000
0.005
0.010
0.015
0.020
0.025
Cysteine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.01
0.00
0.01
0.02
0.03
0.04
0.05
0.06
Glutamate
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.01
0.00
0.01
0.02
0.03
0.04Glutamine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.1
0.0
0.1
0.2
0.3
0.4
0.5
Glycine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
-0.002
0.000
0.002
0.004
0.006
0.008
0.010
0.012 Histidine
Frequency
Am
plit
ud
e
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.005
0.000
0.005
0.010
0.015
0.020
0.025
Isoleucine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.01
0.00
0.01
0.02
0.03
0.04Leucine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.01
0.00
0.01
0.02
0.03
0.04
0.05Lysine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6
-0.002
0.000
0.002
0.004
0.006
0.008
0.010
0.012
0.014 Methionine
Frequency
Am
plit
ude
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.005
0.000
0.005
0.010
0.015
0.020Phenyalanine
Frequency
Am
plit
ud
e
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.05
0.00
0.05
0.10
0.15
0.20
0.25Proline
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7-0.01
0.00
0.01
0.02
0.03
0.04
0.05Serine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
0.00
0.01
0.02
0.03
0.04
Threonine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
0.000
0.002
0.004
0.006
0.008Tryptophan
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
0.000
0.005
0.010
0.015
0.020
Tyrosine
Frequency
Am
plitu
de
-0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
0.00
0.01
0.02
0.03
0.04Valine
Frequency
Am
plitu
de
Colagen α1(I) uman
200 400 600 800 1000 1200 14000
5
10
15
20
25
30Alanine
Distance
200 400 600 800 1000 1200 14000
2
4
6
8
10
12
14Arginine
Distance
200 400 600 800 1000 1200 14000.0
0.5
1.0
1.5
2.0
2.5
3.0Aspargine
Distance
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Tyrosine
Distance
200 400 600 800 1000 1200 14000
50
100
150
200
250
300
350Glycine
Distance
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Histidine
Distance
200 400 600 800 1000 1200 14000.0
0.5
1.0
1.5
2.0
2.5
3.0Isoleucine
Distance
200 400 600 800 1000 1200 14000
1
2
3
4
5
6
7Leucine
Distance
200 400 600 800 1000 1200 14000
1
2
3
4
5
6
7Lysine
Distance
200 400 600 800 1000 1200 14000.0
0.5
1.0
1.5
2.0Methionine
Distance
200 400 600 800 1000 1200 14000
1
2
3
4
5
6
7
8Aspartate
Distance
200 400 600 800 1000 1200 14000.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0Cysteine
Distance200 400 600 800 1000 1200 1400
0
2
4
6
8
10
12Glutamate
Distance
200 400 600 800 1000 1200 14000
1
2
3
4
5
6Glutamine
Distance
200 400 600 800 1000 1200 14000
1
2
3
4
5Phenyalanine
Distance
200 400 600 800 1000 1200 14000
20
40
60
80
100
Proline
Distance
200 400 600 800 1000 1200 14000
1
2
3
4
5
6
7
8Serine
Distance
200 400 600 800 1000 1200 14000
1
2
3
4
5Threonine
Distance
200 400 600 800 1000 1200 14000.0
0.2
0.4
0.6
0.8
1.0Tryptophan
Distance
200 400 600 800 1000 1200 14000
1
2
3
4
5
6
7Valine
Distance
Distante intre aminoacizi de acelasi tip:
Colagen α1(I) umanProbabilitati de legare intre doi aminoacizi X si Y in lantul de colagen α1(I) uman :
PrLegXY LegYX
obNrX NrY
LegXY= nr de legaturi X-Y LegYX= nr de legaturi Y-XNrX= numarul de aminoacizi X din lantul colagenului NrY= numarul de aminoacizi Y din lantul colagenului
Interferon β
P01574 IFNB_HUMAN
A 8
R 11
N 13
D 5
C 5
Q 12
E 13
G 6
H 5
I 12
L 30
K 12
M 5
F 10
P 1
S 11
T 10
W 3
Y 10
V 5
MTNKCLLQIALLLCFSTTALSMSYNLLGFLQRSSNFQCQKLLWQLNGRLEYCLKDRMNFDIPEEIKQLQQFQKEDAALTIYEMLQNIFAIFRQDSSSTGWNETIVENLLANVYHQINHLKTVLEEKLEKEDFTRGKLMSSLHLKRYYGRILHYLKAKEYSHCAWTIVRVEILRNFYFINRLTGYLRN
187 aminoacizi
Interferon β
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0Alanine
Chain Position
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0Arginine
Chain Position20 40 60 80 100 120 140 160 180
0.0
0.2
0.4
0.6
0.8
1.0Aspargine
Chain Position
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Aspartate
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Cysteine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Glutamate
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Glutamine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chin Position
Glycine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Histidine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Isoleucine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Leucine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Lysine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Methionine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Phenylalanine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Proline
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Serine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Threonine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Tryptophan
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Tyrosine
20 40 60 80 100 120 140 160 1800.0
0.2
0.4
0.6
0.8
1.0
Chain Position
Valine
Pozitionari in lant:
Interferon β
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08Alanine
Frequency
Am
plit
ud
e
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08
Arginine
Frequency
Am
plitu
de0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08Aspargine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.60.00
0.01
0.02
0.03
0.04
0.05
Aspartate
Frequency
Am
plitu
de
0.0 0.2 0.4 0.60.00
0.01
0.02
0.03
0.04
0.05
Cysteine
Frequency
Am
plit
ud
e
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08Glutamate
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08Glutamine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6-0.01
0.00
0.01
0.02
0.03
0.04
0.05
0.06
Glycine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6-0.01
0.00
0.01
0.02
0.03
0.04
0.05
0.06
Histidine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.60.00
0.02
0.04
0.06
0.08
Isoleucine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6
0.00
0.05
0.10
0.15
Leucine
Frequency
Am
plit
ud
e
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08
Lysine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6-0.01
0.00
0.01
0.02
0.03
0.04
0.05
0.06
Methionine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.60.00
0.02
0.04
0.06
0.08
Phenylalanine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.60.004
0.006
0.008
0.010
0.012
Proline
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08Serine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08
Threonine
Frequency
Am
plit
ud
e
0.0 0.2 0.4 0.6
0.00
0.01
0.02
0.03
0.04
Tryptophan
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08
Tyrosine
FrequencyA
mp
litu
de
0.0 0.2 0.4 0.60.00
0.01
0.02
0.03
0.04
0.05
Valine
Frequency
Am
plitu
de
FFT:
Concluzii
• Aplicarea metodelor statistice in moleculele cu lanturi mari permite obtinerea de argumente pentru ordonarea partiala a aminoacizilor si obtinerea de corelatii intre aminoacizi.
• Atunci cand aminoacizii sunt folositi pentru construirea unor lanturi lungi si complicate metodele statistice sunt eficiente pentru dezvaluirea structurii primare a biomoleculelor.
Va multumesc pentru atentie!
