Wrong assumptions and misinterpretations in explanations of biological models, phenomena and...

Wrong assumptions and misinterpretations

in explanations of biological models, phenomena and processes

Jacek LelukICM UW

orIs biologist logical,

and computer scientist alive?

How is it, that your genome is in 98% the same as genome of

chimpanzee and only in 50% as your own father’s genome?

"O składności członów człowieczych"

Dlaczego ptacy mleka nie dają?

Bo musiałyby mieć cyce, które by im wadziły ku lataniu.

Andrzej z Kobylina (XVI w.)

Is biology „bilogical”?Nomenclature chaos:• Mitochondria or chondriosomes?• Is papain a proteolytic enzyme?• definition of identity, similarity an homologyMisinterpretaion:• Amino acid sequence of gene?• Why squash inhibitors are inhibitors?• Is wheat aglutinin to aglutinate rabbit red cells?Incomplete knowledge• Stochastic index matrices• Statistical description of biological processes

The problem of terminology

• BPTI - Basic Pancreatic Trypsin Inhibitor - Bovine Pancreatic Trypsin Inhibitor - Basic Protein Trypsin Inhibitor

• PAM- Point Accepted Mutations- Percent Accepted Mutations

• Kunitz trypsin inhibitor- BPTI - mammalian organs- STI - soybean trypsin inhibitor

What may everybody do wrong?

Monte Carlo approach in structure analysis and prediction - – what state do we predict?

Mathematical modelling of life processes – - Markov chains and protein evolution and differentiation- significance similarity estimation

What may biologists do wrong?

Amino acids and proteins – - do proteins consist of amino acids as we describe?

Definitions and theory –- definition of species and theory of evolution- definitions and biology

Correlated mutations –- dispersed correlation

What may theoreticians do wrong?

Primitive or ancestral? –- (Cyanophyta, Archaebacteria, ape and human)

Global and local energy minima –- can we predict the exact conformation at exact time?

Microscopic/mesoscopic/macroscopic processes - - water molecule and tsunami

Assumptions and conclusions –- incomplete assumptions and wrong conclusions- deformations by simplifying- is the protein sequence just a string of characters?

Sequence identity estimation in proteomics and genomics

Identity threshold – does it make sense?

WHAT IS IMPORTANT IN THE PROTEIN SIMILARITY SEARCH ?

1) Contribution (%) of identical positions

2) Length of the compared strings (sequences)

3) Distribution of the identical positions along the analyzed sequence

WHAT IS IMPORTANT IN THE PROTEIN SIMILARITY SEARCH ? 1) Contribution (%) of identical positions PKILMECKKD 8 PKILMECKKD 2 PKILMKCKHD 80% SDCLLDCVCL 20% similar not similar 2) Length of the compared strings (sequences) LCE 1 MVEICIEPKIRCIKVCTKDERITCLILDET 8 WCG 33.3% MVYWCPRRFMHCVHLKAGGCTCWCLRLDYY 26% casual probably similar 3) Distribution of the identical positions along the analyzed sequence MVEMICIEPKIRCIKVCTKDERITL 5 MVEMIMAGDARCIKVCTKDERITCL 5 HVYYWRPERFMHTVKLKAGGCRCWL 20% HHYYWMAGDAHTVQLKAGGCWCWAG 20% casual similar 4) Residues at conservative positions MVCPKILMKCKHDSDCLLDCVCLED MVCPKILMKCKHDSDTLLDCVCLED EDEGKRRTKREHFKESNLAAAFKEQ QNCPGPREWCFTTRMNDSSCACPQT not similar similar 5) Structural/genetic similarity of the amino acids at non-conservative positions

Identity only

MVCPKILMKCKHDSDCLLDCVCLED RLCRRLVKRCRKETECIVECICIDE

Structural Genetic MVCPKILMKCKHDSDCLLDCVCLED MVCPKILMKCKHDSDCLLDCVCLED RLCRRLVKRCRKETECIVECICIDE RLCRRLVKRCRKETECIVECICIDE


Identity only




Identity only



WHAT IS IMPORTANT IN THE PROTEIN SIMILARITY SEARCH ?

4) Residues at the conservative positions

5) Structural/genetic similarity of the amino acids at non-conservative positions


Identity only




Identity only



Sequence multiple alignment

Problem of gap manipulation

Any protein can be aligned with each other as homologous/similar

anybiologicalstring anybilogicalstrip

anybiologicalstri-ng anybi-logicalstrip

anyproteincanbealigned

-an-yprote--i-ncanb-----ealigned

Statistical approaches vs. accuracyHow far may they be improved?

Protein secondary structure prediction – accuracy 70-72%(not much changed since 1978)

100% accuracy requires the complete database for all possible structures.

For 30 AA polypeptides – 2030 sequences/secondary structures

Searching the database for appropriate sequence/structure with the rate 1012 sequences/sec. would proceed 1.8 bilion times longer than the age

of the Universe.

Genetic conditioning of the amino acid replacement probabilities and

spectrum in molecular evolution

The Markov model assumes that the substitution probability of amino acid AA1 by AA2 is the same, regardless of what the initial

residue AA1 was transformed from (AAx, AAy)

The currently used statistical algorithms are based on Markovian model of the amino acid replacement (they directly use stochastic

matrices of replacement frequency indices)

AA1 AA2AAx

Pa

AA1 AA2AAy

Pb

Pa = Pb

BLOSUM62 matrix of amino acid replacements

A 4 R -1 5 N -2 0 6 D -2 -2 1 6 C 0 -3 -3 -3 9 Q -1 1 0 0 -3 5 E -1 0 0 2 -4 2 5 G 0 -2 0 -1 -3 -2 -2 6 H -2 0 1 -1 -3 0 0 -2 8 I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4

A R N D C Q E G H I L K M F P S T W Y V

Why tryptophane is here the most conservative residue?

Replacemant Arg Lys according to the statistical interpretation using stochastical matrix indices

Arg Lys

PAM250 3

BLOSUM62 2

BLOSUM35 2

BLOSUM45 3

BLOSUM100 3

Arginine-to-lysine mutational replacements

GlnCAR

ArgAGR

ArgAGR

SerAGY

ArgCGR

HisCAY

LysAARCGY

Arg

LeuCTR

LysAARCGR

Arg

MetATG

LysAAGAGG

Arg

Thr

Ser

SerUCG

SerAGU

Ile Asn

Arg Cys

Gly

TrpUGG

AlaThr Pro

TrpSer Leu

(UAG)

AsnAAU

Possible one-point-mutational processing of serine with respect to its origin

Possible codons for arginine: AGA AGG CGA CGG CGC CGT

Is arginine the same as arginine?

AGCU 1

3 2

Q

Q

H

H

–

–

Y

Y

E

E

D

D

K

K

N

N

R

R

R

R

–

W

C

C

G

G

G

G

R

R

S

S

P

P

P

P

S

S

S

S

A

A

A

A

T

T

T

T

L

L

L

L

L

L

F

F

V

V

V

V

I

M

I

I

Diagram of amino acid genetic relationships CAA UAA GAA AAA

CAG UAG GAG AAG

CAC UAC GAC AAC

CAU UAU GAU AAU

CGA UGA GGA AGA

CGG UGG GGG AGG

CGC UGC GGC AGC

CGU UGU GGU AGU

CCA UCA GCA ACA

CCG UCG GCG ACG

CCC UCC GCC ACC

CCU UCU GCU ACU

CUA UUA GUA AUA

CUG UUG GUG AUG

CUC UUC GUC AUC

CUU UUU GUU AUU

Diagram of codon genetic relationships

H

H

–

–

Y

Y

E

E

D

D

K

K

N

N

R

R

–

W

C

C

G

G

G

G

R

S

S

P

P

P

P

S

S

S

S

A

A

A

A

T

T

T

T

L

L

L

L

L

L

F

F

V

V

V

V

I

I

I

AGCU 1

3 2

Genetic relationships between Arg and Met/Gln

M

R

R

Q

R

Q

What part of the codon contains the information about the previous amino acid that occurred at certain position of the

protein sequence?

At most 2/3 of the entire codon.

AlaGCG

ValGUG

How long is the information about codons of preceeding amino acids stored?

Theoreticaly the longest period is infinite

The shortest storage period is 3 transitions/transversions

AlaGCG

ValGUG

MetAUG

IleAUA

SerUCC

SerUCU

ThrACU

SerAGU

LysAAA

AsnAAC

AspGAC

HisCAC

GlnCAG

GluGAG

AspGAU

HisCAU

AsnAAU

LysAAG

GlnCAG

HisCAC

TyrUAU . . .

Correlated mutations

The phenomenon of several mutations occurring simultaneously and dependent on each other

According to the current hypothesis of molecular positive Darwinian selection, correlated mutations are related to the changes

occurring in their neighborhood, they reflect the protein-to-protein interaction and they preserve the biological activity

and structural properties of the molecule

The current explanation of correlated mutations occurrence (example)

CH2

HN

CH2

CHCH3H3C

Trp

Leu

CH

CH3H3C

CH3

Ala

Val

CH

CH3H3C

CH2

CHCH3H3C

Val

Leu

CH2

HN

CH3

Ala

Trp

The three types of distribution of correlated positions present in myoglobins

The residue location and relative distribution is shown on tertiary structure of human myoglobin (P0244, pdb1bzp)

The spot correlation cluster

Position no. and occurring residues

Correlation versus position 127

127 [AMSTV] A (58) S (7)

27 [ADEFLNT] ADEFNT E

31 [GKRS] GKRS R

78 [AKLQ] K ALQ

109 [DEGNT] DEGT E

116 [AEHKQST] AEHKQS A

117 [AEKNQS] AEKQS E

122 [BDEN] BDEN D

C:\ppt\pliki\Myoglobin_s.EXE

The three types of distribution of correlated positions present in Bowman-Birk inhibitor family

The residue location and relative distribution is shown on tertiary structure of Bowman-Birk inhibitor from soybean (P01055)

The narrow correlation cluster



13 [–ADFIKLMPRSTV] L (11) M (10)

A (8)

4 [–RSTVY] V –S S

5 [–KPST] K –S S

7 [AEGKP] A P P

11 [EFHIKLQRST] T EHQ S

21 [EFIKMQT] T Q EQ

C:\ppt\pliki\bbi_n.EXE

The three types of distribution of correlated positions present in eglin-like proteins.

The residue location and relative distribution is shown on tertiary structure of eglin C (P01051)



67 [–DGNT] D (8) G (9)

10 [–ELNQRST] ET LNQRS

The dispersed correlation

C:\ppt\pliki\Eglin_d.EXE

The three types of distribution of correlated positions present in lysozymes

The residue location and relative distribution is shown on tertiary structure of lysozyme from rat (P00697, pdb5lyz)

The dispersed correlation



80 [GHKNR] G (7) H (31) N (16)

30 [ILMV] MV ILMV V

40 [DFKNR] DN N FKNR

C:\ppt\pliki\Lysozyme_d.EXE

The observed number and contribution of three correlation types in four different protein families

The correlation sets consist of 2 to over 20 residues

The protein

family (number of correlated

positions/set)

The correlation statistics

Total number of correlation

sets observed

Number of dispersed

sets

Number of narrow clusters

Number of undirected

clusters

Number of sets

related to active center

Eglin-like proteins (2-13) 20 7 7 6 1

Bowman-Birk proteinase

inhibitors (2-28)23 4 13 6 9

Myoglobins (2-29)

41 23 9 9 n.a.

Lysozymes (2-15) 41 25 9 7 9

All families 125 (100%) 59 (47.2%) 38 (30.4%) 28 (22.4%) -

Bowls are concave

Bowls are convex

A mathematician – biologist dialogueThe communication problem

...not always the first conclusion is correct and the first impression consistent with the reality

In entire splendour of natural phenomena...

Zestawienie sekwencji (multiple alignment) 52 inhibitorów proteinaz typu Bowman-Birk sporządzone za pomocą algorytmu

semihomologii genetycznej Reszty konserwatywne i typowe wyszczególniono białymi literami na czarnym tle. Szare tło wskazuje aminokwasy

semihomologiczne. 3 10 20 30 40 50 60 P01055 ESSKPCCDQCACTKSNPPQCRCSDMRLNSCHSACKSCICALSYPAQCF-CVDITDFCYEP-CKP P01057 ESSKPCCDECACTKSIPPQCRCTDVRLNSCHSACSSCVCTFSIPAQCV-CVDMKDFCYAP-CKS P01056 QSSKPCCBHCACTKSIPPQCRCTDLRLDSCHSACKSCICTLSIPAQCV-CBBIBDFCYEP-CKS P01058 ESSKPCCDQCSCTKSMPPKCRCSDIRLNSCHSACKSCACTYSIPAKCF-CTDINDFCYEP-CKS P01059 ESSKPCCDLCTCTKSIPPQCHCNDMRLNSCHSACKSCICALSEPAQCF-CVDTTDFCYKS-CHN P01063 ESSKPCCDLCMCTASMPPQCHCADIRLNSCHSACDRCACTRSMPGQCR-CLDTTDFCYKP-CKS P17734 QSSKPCCRQCACTKSIPPQCRCSQVRLNSCHSACKSCACTFSIPAQCF-CGBIBBFCYKP-CKS P81483 -SSKPCCBHCACTKSIPPQCRCSBLRLNSCHSECKGCICTFSIPAQCI-CTDTNNFCYEP-CKS P81484 -SSKPCCBHCACTKSIPPQCRCSBLRLNSCHSECKGCICTFSIPAQCI-CTDTNNFCYEP-CKS P16343 ESSKPCCSSC-CTRSRPPQCQCTDVRLNSCHSACKSCMCTFSDPGMCS-CLDVTDFCYKP-CKS P01064 EYSKPCCDLCMCTRSMPPQCSCEDIRLNSCHSDCKSCMCTRSQPGQCR-CLDTNDFCYKP-CKS P82469 -SSGPCCDRCRCTKSEPPQCQCQDVRLNSCHSACEACVCSHSMPGLCS-CLDITHFCHEP-CKS P01061 ESSHPCCDLCLCTKSIPPQCQCADIRLDSCHSACKSCMCTRSMPGQCR-CLDTHDFCHKP-CKS P01062 ESSEPCCDSCDCTKSIPPECHCANIRLNSCHSACKSCICTRSMPGKCR-CLDTDDFCYKP-CES P01060 QSSPPCCBICVCTASIPPQCVCTBIRLBSCHSACKSCMCTRSMPGKCR-CLBTTBYCYKS-CKS 1BBI: ESSKPCCDQCACTKSNPPQCRCSDMRLNSCHSACKSCICALSYPAQCF-CVDITDFCYEP-CKP 1D6R:I ---KPCCDQCACTKSNPPQCRCSDMRLNSCHSACKSCICALSYPAQCF-CVDITDFCYEP-CK- 1DF9:C ESSEPCCDSCDCTKSIPPQCHCANIRLNSCHSACKSCICTRSMPGKCR-CLDTDDFCYKP-CES 1PI2: EYSKPCCDLCMCTRSMPPQCSCED-RINSCHSDCKSCMCTRSQPGQCR-CLDTNDFCYKP-CKS 1PBI:A DVKSACCDTCLCTKSNPPTCRCVDVGET-CHSACLSCICAYSNPPKCQ-CFDTQKFCYKQ-CHN AAB4719 ESSKPCCDQCTCTKSIPPQCRCTDVRLNSCHSACSSCVCTFSIPAQCV-CVDMKDFCYAP-CKS TISYC2 ESSKPCCDLCMCTASMPPQCHCADIRLNSCHSACDRCACTRSMPGQCR-CLDTTDFCYKP-CKS JC2225 ESSKPCCDLCMCTASMPPQCHCADIRLNSCHSACDRCACTRSMPGQCR-CLDTTDFCYKP-CKS TIZB2 ESSKPCCDQC-CTKSMPPKCRCSDIRLDSCHSACKSCACTYSIPAKCF-CTDINDFCYEP-CKS JC2073 ESSKPCCDECKCTKSEPPQCQCVDTRLESCHSACKLCLCALSFPAKCR-CVDTTDFCYKP-CKS JC2072 ESSKPCCDECKCTKSEPPQCQCVDTRLESCHSACKLCLCALSFPAKCR-CVDTTDFCYKP-CKS 0506164 ESSKPCCDQC-CTKSMPPKCRCSDIRLDSCHSACKSCACTYSIPAKCF-CTDINDFCYEP-CKS 0401177 ESSKPCCDLCMCTASMPPQCHCADIRLNSCHSACDRCACTRSMPGQCR-CLDTTDFCYKP-CKS 763679A ESSKPCCDLCMCTASMPPQCHCADIRLNSCHSACDRCACTRSMPGQCR-CLDTTDFCYKP-CKS TISYD2 EYSKPCCDLCMCTRSMPPQCSCEDIRLNSCHSDCKSCMCTRSQPGQCR-CLDTNDFCYKP-CKS 0907248 ESSEPCCDSCRCTKSIPPQCHCADIRLNSCHSACKSCMCTRSMPGKCR-CLDTDDFCYKP-CES 1102213 ESSEPCCDLCLCTKSIPPQCQCADIRLNSCHSACKSCMCTRSMPGQCH-CLDTHDFCHKP-CKS 1102213 ESSEPCCDLCLCTKSIPPQCQCADIRLNSCHSACKSCMCTRSMPGQCR-CLDTHDFCHKP-CKS 0404180 EYSKPCCDLCMCTRSMPPQCSCEDIRLNSCHSDCKSCMCTRSQPGQCR-CLDTNDFCYKP-CKS TIZB1B ESSHPCCDLCLCTKSIPPQCQCADIRLDSCHSACKSCMCTRSMPGQCH-CLDTHDFCHKP-CKS TIMB ESSEPCCDSCDCTKSKPPQCHCANIRLNSCHSACKSCICTRSMPGKCR-CLDTDDFCYKP-CES TIZB1P ESSHPCCDLCLCTKSIPPQCQCADIRLNSCHSACKSCMCTRSMPGQCR-CLDTHDFCHKP-CKS JC1066 ESSEPCCDSCDCTKSKPPQCHCANIRLNSCHSACKSCICTRSMPGKCR-CLDTDDFCTKP-CES Q41066 DVKSACCDTCLCTKSDPPTCRCVDVGET-CHSACDSCICALSYPPQCQ-CFDTHKFCYKA-CHN P80321 STTTACCDFCPCTRSIPPQCQCTDVREK-CHSACKSCLCTLSIPPQCH-CYDITDFCYPS-CR- Q41065 DVKSACCDTCLCTKSNPPTCRCVDVRET-CHSACDSCICAYSNPPKCQ-CFDTHKFCYKA-CHN P81705 --TSACCDKCFCTKSNPPICQCRDVGET-CHSACKFCICALSYPAQCH-CLDQNTFCYDK-CDS P56679 DVKSACCDTCLCTKSNPPTCRCVDVGET-CHSACLSCICAYSNPPKCQ-CFDTQKFCYKA-CHN P16346 --TTACCNFCPCTRSIPPQCRCTDIGET-CHSACKTCLCTKSIPPQCH-CADITNFCYPK-CN- P01065 DVKSACCDTCLCTRSQPPTCRCVDVGER-CHSACNHCVCNYSNPPQCQ-CFDTHKFCYKA-CHS P24661 DVKSACCDTCLCTKSEPPTCRCVDVGER-CHSACNSCVCRYSNPPKCQ-CFDTHKFCYKS-CHN P07679 KRPWECCDIAMCTRSIPPICRCVDKVDR-CSDACKDCEETEDN--RHV-CFDTYIGDPGPTCHD P19860 ERPWKCCDLQTCTKSIPAFCRCRDLLEQ-CSDACKECGKVRDSDPPRYICQDVYRGIPAPMCHE P22737 ERPWKCCDLQTCTKSIPAFCRCRDLLEQ-CSDACKECGKVRDSDPPRYICQDVYRGIPAPMCHE 220645 ES-EGCCDRCICTKSMPPQCHCHDVRLDSCHSDCETCICTRSYPAQCR-CADTTDFCYKP-C-S P09864 TRPWKCCDRAICTKSFPPMCRCMDMVEQ-CAATCKKCGPATSDSSRRV-CEDXY----------- P09863 KRPWKCCDQAVCTRSIPPICRCMDQVFE-CPSTCKACGPSVGDPSRRV-CQDQYV---------- KONSENSUS ESSKPCCDXCXCTKSIPPQCRCXDXRLNSCHSACKSCXCTRSXPXQCX-CXDTXDFCYKP-CKS

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Wrong assumptions and misinterpretations in explanations of biological models, phenomena and...

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