Regularitati ascunse si corelatii in nano-bio-structuri M.pdf · Regularitati ascunse si corelatii...
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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
Transcript of Regularitati ascunse si corelatii in nano-bio-structuri M.pdf · Regularitati ascunse si corelatii...
Regularitati ascunse sicorelatii in nano-bio-structuri
M. Popescu, A. Velea
NATIONAL INSTITUTE OF MATERIALS PHYSICSBUCHAREST-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 nn n
AX t A n t B n tω ω∞ ∞
= =
= + +∑ ∑
0
/2
/2
1 1( ) ( ) ( )2
Tin t
n nT
G f A iB X t e dtT
ω+
−
= + = ∫ 0f nω=
02Tπω =
Colagen α1(I) uman
47V
13Y
6W
45T
60S
278P
27F
13M
57K
48L
24I
9H
391G
75E
49Q
18C
66D
28N
71R
139AMFSFVDLRLLLLLAATALLTHGQEEGQVEGQDEDIPPITCVQNGLRYHDRDVWKPEPCRICVCDNGKVLCDDVICDETKNCPGAEVPEGECCPVCPDGSESPTDQETTGVEGPKGDTGPRGPRGPAGPPGRDGIPGQPGLPGPPGPPGPPGPPGLGGNFAPQLSYGYDEKSTGGISVPGPMGPSGPRGLPGPPGAPGPQGFQGPPGEPGEPGASGPMGPRGPPGPPGKNGDDGEAGKPGRPGERGPPGPQGARGLPGTAGLPGMKGHRGFSGLDGAKGDAGPAGPKGEPGSPGENGAPGQMGPRGLPGERGRPGAPGPAGARGNDGATGAAGPPGPTGPAGPPGFPGAVGAKGEAGPQGPRGSEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGAKGANGAPGIAGAPGFPGARGPSGPQGPGGPPGPKGNSGEPGAPGSKGDTGAKGEPGPVGVQGPPGPAGEEGKRGARGEPGPTGLPGPPGERGGPGSRGFPGADGVAGPKGPAGERGSPGPAGPKGSPGEAGRPGEAGLPGAKGLTGSPGSPGPDGKTGPPGPAGQDGRPGPPGPPGARGQAGVMGFPGPKGAAGEPGKAGERGVPGPPGAVGPAGKDGEAGAQGPPGPAGPAGERGEQGPAGSPGFQGLPGPAGPPGEAGKPGEQGVPGDLGAPGPSGARGERGFPGERGVQGPPGPAGPRGANGAPGNDGAKGDAGAPGAPGSQGAPGLQGMPGERGAAGLPGPKGDRGDAGPKGADGSPGKDGVRGLTGPIGPPGPAGAPGDKGESGPSGPAGPTGARGAPGDRGEPGPPGPAGFAGPPGADGQPGAKGEPGDAGAKGDAGPPGPAGPAGPPGPIGNVGAPGAKGARGSAGPPGATGFPGAAGRVGPPGPSGNAGPPGPPGPAGKEGGKGPRGETGPAGRPGEVGPPGPPGPAGEKGSPGADGPAGAPGTPGPQGIAGQRGVVGLPGQRGERGFPGLPGPSGEPGKQGPSGASGERGPPGPMGPPGLAGPPGESGREGAPGAEGSPGRDGSPGAKGDRGETGPAGPPGAPGAPGAPGPVGPAGKSGDRGETGPAGPTGPVGPVGARGPAGPQGPRGDKGETGEQGDRGIKGHRGFSGLQGPPGPPGSPGEQGPSGASGPAGPRGPPGSAGAPGKDGLNGLPGPIGPPGPRGRTGDAGPVGPPGPPGPPGPPGPPSAGFDFSFLPQPPQEKAHDGGRYYRADDANVVRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGESMTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQNITYHCKNSVAYMDQQTGNLKKALLLQGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKTSRLPIIDVAPLDVGAPDQEFGFDVGPVCFL
1464 aminoacizi
CO1A1_HUMANP02452
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 Position200 400 600 800 1000 1200 1400
0.0
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 Position200 400 600 800 1000 1200 1400
0.0
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 Position 200 400 600 800 1000 1200 14000.0
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
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
0.06Arginine
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
0.025Aspargine
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
0.05Aspartate
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
0.025Cysteine
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
0.06Glutamate
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
Ampl
itude
-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
0.5Glycine
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
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
0.025Isoleucine
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
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
0.020Phenyalanine
Frequency
Am
plitu
de
-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
0.04Threonine
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
0.020Tyrosine
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
Distance200 400 600 800 1000 1200 1400
0
2
4
6
8
10
12
14 Arginine
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
Distance200 400 600 800 1000 1200 1400
0.0
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
Distance200 400 600 800 1000 1200 1400
0
1
2
3
4
5
6
7Leucine
Distance200 400 600 800 1000 1200 1400
0
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 :
Pr LegXY LegYXobNrX NrY
+=+
LegXY= nr de legaturi X-Y LegYX= nr de legaturi Y-XNrX= numarul de aminoacizi X din lantul colagenuluiNrY= numarul de aminoacizi Y din lantul colagenului
Interferon β
IFNB_HUMANP01574
5V
10Y
3W
10T
11S
1P
10F
5M
12K
30L
12I
5H
6G
13E
12Q
5C
5D
13N
11R
8A
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 Position 20 40 60 80 100 120 140 160 1800.0
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
plitu
de
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08Arginine
Frequency
Am
plitu
de
0.0 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
0.05Cysteine
Frequency
Am
plitu
de
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
0.06Glycine
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
0.08Isoleucine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6
0.00
0.05
0.10
0.15
Leucine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08
Lysine
Frequency
Ampl
itude
0.0 0.2 0.4 0.6-0.01
0.00
0.01
0.02
0.03
0.04
0.05
0.06Methionine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.60.00
0.02
0.04
0.06
0.08Phenylalanine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.60.004
0.006
0.008
0.010
0.012Proline
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
plitu
de
0.0 0.2 0.4 0.6
0.00
0.01
0.02
0.03
0.04Tryptophan
Frequency
Am
plitu
de
0.0 0.2 0.4 0.6
0.00
0.02
0.04
0.06
0.08Tyrosine
Frequency
Am
plitu
de
0.0 0.2 0.4 0.60.00
0.01
0.02
0.03
0.04
0.05Valine
Frequency
Ampl
itude
FFT:
Concluzii
• Aplicarea metodelor statistice in moleculele cu lanturi mari permite obtinerea de argumentepentru ordonarea partiala a aminoacizilor siobtinerea de corelatii intre aminoacizi.
• Atunci cand aminoacizii sunt folositi pentruconstruirea unor lanturi lungi si complicate metodele statistice sunt eficiente pentrudezvaluirea structurii primare a biomoleculelor.
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