|1.||Kochańczyk M., Kocieniewski P., Kozłowska E., Jaruszewicz-Błońska J., Sparta B., Pargett M., Albeck J.G., Hlavacek W.S., Lipniacki T., Relaxation oscillations and hierarchy of feedbacks in MAPK signaling, Scientific Reports, ISSN: 2045-2322, DOI: 10.1038/srep38244, Vol.7, No.38244, pp.1-15, 2017|Kochańczyk M.
, Kocieniewski P.
, Kozłowska E., Jaruszewicz-Błońska J.
, Sparta B., Pargett M., Albeck J.G., Hlavacek W.S., Lipniacki T.
, Relaxation oscillations and hierarchy of feedbacks in MAPK signaling
, Scientific Reports
, ISSN: 2045-2322
, DOI: 10.1038/srep38244
, Vol.7, No.38244, pp.1-15, 2017
We formulated a computational model for a MAPK signaling cascade downstream of the EGF receptor to investigate how interlinked positive and negative feedback loops process EGF signals into ERK pulses of constant amplitude but dose-dependent duration and frequency. A positive feedback loop involving RAS and SOS, which leads to bistability and allows for switch-like responses to inputs, is nested within a negative feedback loop that encompasses RAS and RAF, MEK, and ERK that inhibits SOS via phosphorylation. This negative feedback, operating on a longer time scale, changes switch-like behavior into oscillations having a period of 1 hour or longer. Two auxiliary negative feedback loops, from ERK to MEK and RAF, placed downstream of the positive feedback, shape the temporal ERK activity profile but are dispensable for oscillations. Thus, the positive feedback introduces a hierarchy among negative feedback loops, such that the effect of a negative feedback depends on its position with respect to the positive feedback loop. Furthermore, a combination of the fast positive feedback involving slow-diffusing membrane components with slower negative feedbacks involving faster diffusing cytoplasmic components leads to local excitation/global inhibition dynamics, which allows the MAPK cascade to transmit paracrine EGF signals into spatially non-uniform ERK activity pulses.
MAPK signaling, Oscillations, Mathematical modelling
|2.||Varga A., Ehrenreiter K., Aschenbrenner B., Kocieniewski P., Kochańczyk M., Lipniacki T., Baccarini M., RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα, Science Signaling, ISSN: 1945-0877, DOI: 10.1126/scisignal.aai8482, Vol.10, No.469, pp.eaai8482-1-11, 2017|
Varga A., Ehrenreiter K., Aschenbrenner B., Kocieniewski P.
, Kochańczyk M.
, Lipniacki T.
, Baccarini M., RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα
, Science Signaling
, ISSN: 1945-0877
, DOI: 10.1126/scisignal.aai8482
, Vol.10, No.469, pp.eaai8482-1-11, 2017
Downstream of growth factor receptors and of the guanine triphosphatase (GTPase) RAS, heterodimers of the serine/threonine kinases BRAF and RAF1 are critical upstream kinases and activators of the mitogen-activated protein kinase (MAPK) module containing the mitogen-activated and extracellular signal–regulated kinase kinase (MEK) and their targets, the extracellular signal–regulated kinase (ERK) family. Either direct or scaffold protein–mediated interactions among the components of the ERK module (the MAPKKKs BRAF and RAF1, MEK, and ERK) facilitate signal transmission. RAF1 also has essential functions in the control of tumorigenesis and migration that are mediated through its interaction with the kinase ROKα, an effector of the GTPase RHO and regulator of cytoskeletal rearrangements. We combined mutational and kinetic analysis with mathematical modeling to show that the interaction of RAF1 with ROKα is coordinated with the role of RAF1 in the ERK pathway. We found that the phosphorylated form of RAF1 that interacted with and inhibited ROKα was generated during the interaction of RAF1 with the ERK module. This mechanism adds plasticity to the ERK pathway, enabling signal diversification at the level of both ERK and RAF. Furthermore, by connecting ERK activation with the regulation of ROKα and cytoskeletal rearrangements by RAF1, this mechanism has the potential to precisely coordinate the proper timing of proliferation with changes in cell shape, adhesion, or motility.
MAPK pathway, kinase RAF, protein isoform, phosphorylation, mathematical modeling
|3.||Hat B., Kochańczyk M., Bogdał M.N., Lipniacki T., Feedbacks, bifurcations, and cell fate decision-making in the p53 system, PLOS COMPUTATIONAL BIOLOGY, ISSN: 1553-734X, DOI: 10.1371/journal.pcbi.1004787, Vol.12, No.2, pp.e1004787-1-28, 2016|Hat B.
, Kochańczyk M.
, Bogdał M.N.
, Lipniacki T.
, Feedbacks, bifurcations, and cell fate decision-making in the p53 system
, PLOS COMPUTATIONAL BIOLOGY
, ISSN: 1553-734X
, DOI: 10.1371/journal.pcbi.1004787
, Vol.12, No.2, pp.e1004787-1-28, 2016
The p53 transcription factor is a regulator of key cellular processes including DNA repair, cell cycle arrest, and apoptosis. In this theoretical study, we investigate how the complex circuitry of the p53 network allows for stochastic yet unambiguous cell fate decision-making. The proposed Markov chain model consists of the regulatory core and two subordinated bistable modules responsible for cell cycle arrest and apoptosis. The regulatory core is controlled by two negative feedback loops (regulated by Mdm2 and Wip1) responsible for oscillations, and two antagonistic positive feedback loops (regulated by phosphatases Wip1 and PTEN) responsible for bistability. By means of bifurcation analysis of the deterministic approximation we capture the recurrent solutions (i.e., steady states and limit cycles) that delineate temporal responses of the stochastic system. Direct switching from the limit-cycle oscillations to the “apoptotic” steady state is enabled by the existence of a subcritical Neimark—Sacker bifurcation in which the limit cycle loses its stability by merging with an unstable invariant torus. Our analysis provides an explanation why cancer cell lines known to have vastly diverse expression levels of Wip1 and PTEN exhibit a broad spectrum of responses to DNA damage: from a fast transition to a high level of p53 killer (a p53 phosphoform which promotes commitment to apoptosis) in cells characterized by high PTEN and low Wip1 levels to long-lasting p53 level oscillations in cells having PTEN promoter methylated (as in, e.g., MCF-7 cell line).
Apoptosis, Cell cycle and cell division, DNA damage, DNA repair, Phosphorylation, Biochemical simulations, Cell cycle inhibitors, Transcription factors
|4.||Korwek Z., Tudelska K., Nałęcz-Jawecki P., Czerkies M., Prus W., Markiewicz J., Kochańczyk M., Lipniacki T., Importins promote high-frequency NF-κB oscillations increasing information channel capacity, Biology Direct, ISSN: 1745-6150, DOI: 10.1186/s13062-016-0164-z, Vol.11, No.61, pp.1-21, 2016|Korwek Z.
, Tudelska K., Nałęcz-Jawecki P., Czerkies M.
, Prus W.
, Markiewicz J.
, Kochańczyk M.
, Lipniacki T.
, Importins promote high-frequency NF-κB oscillations increasing information channel capacity
, Biology Direct
, ISSN: 1745-6150
, DOI: 10.1186/s13062-016-0164-z
, Vol.11, No.61, pp.1-21, 2016
Importins and exportins influence gene expression by enabling nucleocytoplasmic shuttling of transcription factors. A key transcription factor of innate immunity, NF-κB, is sequestered in the cytoplasm by its inhibitor, IκBα, which masks nuclear localization sequence of NF-κB. In response to TNFα or LPS, IκBα is degraded, which allows importins to bind NF-κB and shepherd it across nuclear pores. NF-κB nuclear activity is terminated when newly synthesized IκBα enters the nucleus, binds NF-κB and exportin which directs the complex to the cytoplasm. Although importins/exportins are known to regulate spatiotemporal kinetics of NF-κB and other transcription factors governing innate immunity, the mechanistic details of these interactions have not been elucidated and mathematically modelled.
Based on our quantitative experimental data, we pursue NF-κB system modelling by explicitly including NF-κB-importin and IκBα-exportin binding to show that the competition between importins and IκBα enables NF-κB nuclear translocation despite high levels of IκBα. These interactions reduce the effective relaxation time and allow the NF-κB regulatory pathway to respond to recurrent TNFα pulses of 45-min period, which is about twice shorter than the characteristic period of NF-κB oscillations. By stochastic simulations of model dynamics we demonstrate that randomly appearing, short TNFα pulses can be converted to essentially digital pulses of NF-κB activity, provided that intervals between input pulses are not shorter than 1 h.
By including interactions involving importin-α and exportin we bring the modelling of spatiotemporal kinetics of transcription factors to a more mechanistic level. Basing on the analysis of the pursued model we estimated the information transmission rate of the NF-κB pathway as 1 bit per hour.
Karyopherins, Nucleocytoplasmic transport, Negative feedback, Channel information capacity, Mathematical modelling
|5.||Nałęcz-Jawecki P., Szymańska P., Kochańczyk M., Miękisz J., Lipniacki T., Effective reaction rates for diffusion-limited reaction cycles, JOURNAL OF CHEMICAL PHYSICS, ISSN: 0021-9606, DOI: 10.1063/1.4936131, Vol.143, No.21, pp.215102-1-12, 2015|
Nałęcz-Jawecki P., Szymańska P., Kochańczyk M.
, Miękisz J., Lipniacki T.
, Effective reaction rates for diffusion-limited reaction cycles
, JOURNAL OF CHEMICAL PHYSICS
, ISSN: 0021-9606
, DOI: 10.1063/1.4936131
, Vol.143, No.21, pp.215102-1-12, 2015
Biological signals in cells are transmitted with the use of reaction cycles, such as the phosphorylation-dephosphorylation cycle, in which substrate is modified by antagonistic enzymes. An appreciable share of such reactions takes place in crowded environments of two-dimensional structures, such as plasma membrane or intracellular membranes, and is expected to be diffusion-controlled. In this work, starting from the microscopic bimolecular reaction rate constants and using estimates of the mean first-passage time for an enzyme–substrate encounter, we derive diffusion-dependent effective macroscopic reaction rate coefficients (EMRRC) for a generic reaction cycle. Each EMRRC was found to be half of the harmonic average of the microscopic rate constant (phosphorylation c or dephosphorylation d), and the effective (crowding-dependent) motility divided by a slowly decreasing logarithmic function of the sum of the enzyme concentrations. This implies that when c and d differ, the two EMRRCs scale differently with the motility, rendering the steady-state fraction of phosphorylated substrate molecules diffusion-dependent. Analytical predictions are verified using kinetic Monte Carlo simulations on the two-dimensional triangular lattice at the single-molecule resolution. It is demonstrated that the proposed formulas estimate the steady-state concentrations and effective reaction rates for different sets of microscopic reaction rates and concentrations of reactants, including a non-trivial example where with increasing diffusivity the fraction of phosphorylated substrate molecules changes from 10% to 90%.
Enzymes, Enzyme kinetics, Diffusion, Reaction rate constants, Membrane biochemistry
|6.||Szymańska P., Kochańczyk M., Miękisz J., Lipniacki T., Effective reaction rates in diffusion-limited phosphorylation-dephosphorylation cycles, PHYSICAL REVIEW E, ISSN: 1539-3755, DOI: 10.1103/PhysRevE.91.022702, Vol.91, pp.022702-1-15, 2015|
Szymańska P., Kochańczyk M.
, Miękisz J., Lipniacki T.
, Effective reaction rates in diffusion-limited phosphorylation-dephosphorylation cycles
, PHYSICAL REVIEW E
, ISSN: 1539-3755
, DOI: 10.1103/PhysRevE.91.022702
, Vol.91, pp.022702-1-15, 2015
We investigate the kinetics of the ubiquitous phosphorylation-dephosphorylation cycle on biological membranes by means of kinetic Monte Carlo simulations on the triangular lattice. We establish the dependence of effective macroscopic reaction rate coefficients as well as the steady-state phosphorylated substrate fraction on the diffusion coefficient and concentrations of opposing enzymes: kinases and phosphatases. In the limits of zero and infinite diffusion, the numerical results agree with analytical predictions; these two limits give the lower and the upper bound for the macroscopic rate coefficients, respectively. In the zero-diffusion limit, which is important in the analysis of dense systems, phosphorylation and dephosphorylation reactions can convert only these substrates which remain in contact with opposing enzymes. In the most studied regime of nonzero but small diffusion, a contribution linearly proportional to the diffusion coefficient appears in the reaction rate. In this regime, the presence of opposing enzymes creates inhomogeneities in the (de)phosphorylated substrate distributions: The spatial correlation function shows that enzymes are surrounded by clouds of converted substrates. This effect becomes important at low enzyme concentrations, substantially lowering effective reaction rates. Effective reaction rates decrease with decreasing diffusion and this dependence is more pronounced for the less-abundant enzyme. Consequently, the steady-state fraction of phosphorylated substrates can increase or decrease with diffusion, depending on relative concentrations of both enzymes. Additionally, steady states are controlled by molecular crowders which, mostly by lowering the effective diffusion of reactants, favor the more abundant enzyme.
|7.||Cheng F.H.C., Aguda B.D., Tsai J-C., Kochańczyk M., Lin J.M.J., Chen G.C.W., Lai H-C., Nephew K.P., Hwang T-W., Chan M.W.Y., A Mathematical Model of Bimodal Epigenetic Control of miR-193a in Ovarian Cancer Stem Cells, PLOS ONE, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0116050, Vol.9, No.12, pp.e116050-1-17, 2014|
Cheng F.H.C., Aguda B.D., Tsai J-C., Kochańczyk M.
, Lin J.M.J., Chen G.C.W., Lai H-C., Nephew K.P., Hwang T-W., Chan M.W.Y., A Mathematical Model of Bimodal Epigenetic Control of miR-193a in Ovarian Cancer Stem Cells
, PLOS ONE
, ISSN: 1932-6203
, DOI: 10.1371/journal.pone.0116050
, Vol.9, No.12, pp.e116050-1-17, 2014
Accumulating data indicate that cancer stem cells contribute to tumor chemoresistance and their persistence alters clinical outcome. Our previous study has shown that ovarian cancer may be initiated by ovarian cancer initiating cells (OCIC) characterized by surface antigen CD44 and c-KIT (CD117). It has been experimentally demonstrated that a microRNA, namely miR-193a, targets c-KIT mRNA for degradation and could play a crucial role in ovarian cancer development. How miR-193a is regulated is poorly understood and the emerging picture is complex. To unravel this complexity, we propose a mathematical model to explore how estrogen-mediated up-regulation of another target of miR-193a, namely E2F6, can attenuate the function of miR-193a in two ways, one through a competition of E2F6 and c-KIT transcripts for miR-193a, and second by binding of E2F6 protein, in association with a polycomb complex, to the promoter of miR-193a to down-regulate its transcription. Our model predicts that this bimodal control increases the expression of c-KIT and that the second mode of epigenetic regulation is required to generate a switching behavior in c-KIT and E2F6 expressions. Additional analysis of the TCGA ovarian cancer dataset demonstrates that ovarian cancer patients with low expression of EZH2, a polycomb-group family protein, show positive correlation between E2F6 and c-KIT. We conjecture that a simultaneous EZH2 inhibition and anti-estrogen therapy can constitute an effective combined therapeutic strategy against ovarian cancer.
Ovarian cancer, Messenger RNA, Epigenetics, DNA methylation, Estrogens, Gene expression, Cancer treatment, Carcinogenesis
|8.||Pękalski J., Żuk P.J.♦, Kochańczyk M., Junkin M., Kellogg R., Tay S., Lipniacki T., Spontaneous NF-κB Activation by Autocrine TNFα Signaling: A Computational Analysis, PLOS ONE, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0078887, Vol.8, No.11, pp.e78887-1-14, 2013|
Pękalski J., Żuk P.J.♦
, Kochańczyk M.
, Junkin M., Kellogg R., Tay S., Lipniacki T.
, Spontaneous NF-κB Activation by Autocrine TNFα Signaling: A Computational Analysis
, PLOS ONE
, ISSN: 1932-6203
, DOI: 10.1371/journal.pone.0078887
, Vol.8, No.11, pp.e78887-1-14, 2013
NF-κB is a key transcription factor that regulates innate immune response. Its activity is tightly controlled by numerous feedback loops, including two negative loops mediated by NF-κB inducible inhibitors, IκBα and A20, which assure oscillatory responses, and by positive feedback loops arising due to the paracrine and autocrine regulation via TNFα, IL-1 and other cytokines. We study the NF-κB system of interlinked negative and positive feedback loops, combining bifurcation analysis of the deterministic approximation with stochastic numerical modeling. Positive feedback assures the existence of limit cycle oscillations in unstimulated wild-type cells and introduces bistability in A20-deficient cells. We demonstrated that cells of significant autocrine potential, i.e., cells characterized by high secretion of TNFα and its receptor TNFR1, may exhibit sustained cytoplasmic–nuclear NF-κB oscillations which start spontaneously due to stochastic fluctuations. In A20-deficient cells even a small TNFα expression rate qualitatively influences system kinetics, leading to long-lasting NF-κB activation in response to a short-pulsed TNFα stimulation. As a consequence, cells with impaired A20 expression or increased TNFα secretion rate are expected to have elevated NF-κB activity even in the absence of stimulation. This may lead to chronic inflammation and promote cancer due to the persistent activation of antiapoptotic genes induced by NF-κB. There is growing evidence that A20 mutations correlate with several types of lymphomas and elevated TNFα secretion is characteristic of many cancers. Interestingly, A20 loss or dysfunction also leaves the organism vulnerable to septic shock and massive apoptosis triggered by the uncontrolled TNFα secretion, which at high levels overcomes the antiapoptotic action of NF-κB. It is thus tempting to speculate that some cancers of deregulated NF-κB signaling may be prone to the pathogen-induced apoptosis.
|9.||Kochańczyk M., Jaruszewicz J., Lipniacki T., Stochastic transitions in a bistable reaction system on the membrane, JOURNAL OF THE ROYAL SOCIETY INTERFACE, ISSN: 1742-5689, DOI: 10.1098/rsif.2013.0151, Vol.10, No.84, pp.1-12, 2013|Kochańczyk M.
, Jaruszewicz J.
, Lipniacki T.
, Stochastic transitions in a bistable reaction system on the membrane
, JOURNAL OF THE ROYAL SOCIETY INTERFACE
, ISSN: 1742-5689
, DOI: 10.1098/rsif.2013.0151
, Vol.10, No.84, pp.1-12, 2013
Transitions between steady states of a multi-stable stochastic system in the perfectly mixed chemical reactor are possible only because of stochastic switching. In realistic cellular conditions, where diffusion is limited, transitions between steady states can also follow from the propagation of travelling waves. Here, we study the interplay between the two modes of transition for a prototype bistable system of kinase–phosphatase interactions on the plasma membrane. Within microscopic kinetic Monte Carlo simulations on the hexagonal lattice, we observed that for finite diffusion the behaviour of the spatially extended system differs qualitatively from the behaviour of the same system in the well-mixed regime. Even when a small isolated subcompartment remains mostly inactive, the chemical travelling wave may propagate, leading to the activation of a larger compartment. The activating wave can be induced after a small subdomain is activated as a result of a stochastic fluctuation. Such a spontaneous onset of activity is radically more probable in subdomains characterized by slower diffusion. Our results show that a local immobilization of substrates can lead to the global activation of membrane proteins by the mechanism that involves stochastic fluctuations followed by the propagation of a semi-deterministic travelling wave.
multi-stability, Markov process, spatially extended system, kinetic Monte Carlo on the lattice, kinase autophosphorylation, cell signalling
|10.||Bogdał M.N., Hat B., Kochańczyk M., Lipniacki T., Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate, BMC SYSTEMS BIOLOGY, ISSN: 1752-0509, DOI: 10.1186/1752-0509-7-67, Vol.7, pp.1-17, 2013|Bogdał M.N.
, Hat B.
, Kochańczyk M.
, Lipniacki T.
, Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate
, BMC SYSTEMS BIOLOGY
, ISSN: 1752-0509
, DOI: 10.1186/1752-0509-7-67
, Vol.7, pp.1-17, 2013
Apoptosis is a tightly regulated process: cellular survive-or-die decisions cannot be accidental and must be unambiguous. Since the suicide program may be initiated in response to numerous stress stimuli, signals transmitted through a number of checkpoints have to be eventually integrated.
In order to analyze possible mechanisms of the integration of multiple pro-apoptotic signals, we constructed a simple model of the Bcl-2 family regulatory module. The module collects upstream signals and processes them into life-or-death decisions by employing interactions between proteins from three subgroups of the Bcl-2 family: pro-apoptotic multidomain effectors, pro-survival multidomain restrainers, and pro-apoptotic single domain BH3-only proteins. Although the model is based on ordinary differential equations (ODEs), it demonstrates that the Bcl-2 family module behaves akin to a Boolean logic gate of the type dependent on levels of BH3-only proteins (represented by Bad) and restrainers (represented by Bcl-xL). A low level of pro-apoptotic Bad or a high level of pro-survival Bcl-xL implies gate AND, which allows for the initiation of apoptosis only when two stress stimuli are simultaneously present: the rise of the p53 killer level and dephosphorylation of kinase Akt. In turn, a high level of Bad or a low level of Bcl-xL implies gate OR, for which any of these stimuli suffices for apoptosis.
Our study sheds light on possible signal integration mechanisms in cells, and spans a bridge between modeling approaches based on ODEs and on Boolean logic. In the proposed scheme, logic gates switching results from the change of relative abundances of interacting proteins in response to signals and involves system bistability. Consequently, the regulatory system may process two analogous inputs into a digital survive-or-die decision.
Apoptosis, Cell survival, Signaling pathway, Bcl-2 family, Bistability, Boolean logic, Ordinary differential equations
|11.||Żuk P.J.♦, Kochańczyk M., Jaruszewicz J., Bednorz W., Lipniacki T., Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth–death process, PHYSICAL BIOLOGY, ISSN: 1478-3967, DOI: 10.1088/1478-3975/9/5/055002, Vol.9, pp.055002-1-12, 2012|Żuk P.J.♦
, Kochańczyk M.
, Jaruszewicz J.
, Bednorz W., Lipniacki T.
, Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth–death process
, PHYSICAL BIOLOGY
, ISSN: 1478-3967
, DOI: 10.1088/1478-3975/9/5/055002
, Vol.9, pp.055002-1-12, 2012
Living cells may be considered as biochemical reactors of multiple steady states. Transitions between these states are enabled by noise, or, in spatially extended systems, may occur due to the traveling wave propagation. We analyze a one-dimensional bistable stochastic birth–death process by means of potential and temperature fields. The potential is defined by the deterministic limit of the process, while the temperature field is governed by noise. The stable steady state in which the potential has its global minimum defines the global deterministic attractor. For the stochastic system, in the low noise limit, the stationary probability distribution becomes unimodal, concentrated in one of two stable steady states, defined in this study as the global stochastic attractor. Interestingly, these two attractors may be located in different steady states. This observation suggests that the asymptotic behavior of spatially extended stochastic systems depends on the substrate diffusivity and size of the reactor. We confirmed this hypothesis within kinetic Monte Carlo simulations of a bistable reaction–diffusion model on the hexagonal lattice. In particular, we found that although the kinase–phosphatase system remains inactive in a small domain, the activatory traveling wave may propagate when a larger domain is considered.
multi-stability, Markov process, spatially extended system, kinetic Monte Carlo on the lattice, cell signalling
|12.||Kochańczyk M., Prediction of functionally important residues in globular proteins from unusual central distances of amino acids, BMC STRUCTURAL BIOLOGY, ISSN: 1472-6807, DOI: 10.1186/1472-6807-11-34, Vol.11, pp.34-1-12, 2011|Kochańczyk M.
, Prediction of functionally important residues in globular proteins from unusual central distances of amino acids
, BMC STRUCTURAL BIOLOGY
, ISSN: 1472-6807
, DOI: 10.1186/1472-6807-11-34
, Vol.11, pp.34-1-12, 2011
Well-performing automated protein function recognition approaches usually comprise several complementary techniques. Beside constructing better consensus, their predictive power can be improved by either adding or refining independent modules that explore orthogonal features of proteins. In this work, we demonstrated how the exploration of global atomic distributions can be used to indicate functionally important residues.
Using a set of carefully selected globular proteins, we parametrized continuous probability density functions describing preferred central distances of individual protein atoms. Relative preferred burials were estimated using mixture models of radial density functions dependent on the amino acid composition of a protein under consideration. The unexpectedness of extraordinary locations of atoms was evaluated in the information-theoretic manner and used directly for the identification of key amino acids. In the validation study, we tested capabilities of a tool built upon our approach, called SurpResi, by searching for binding sites interacting with ligands. The tool indicated multiple candidate sites achieving success rates comparable to several geometric methods. We also showed that the unexpectedness is a property of regions involved in protein-protein interactions, and thus can be used for the ranking of protein docking predictions. The computational approach implemented in this work is freely available via a Web interface at http://www.bioinformatics.org/surpresi.
Probabilistic analysis of atomic central distances in globular proteins is capable of capturing distinct orientational preferences of amino acids as resulting from different sizes, charges and hydrophobic characters of their side chains. When idealized spatial preferences can be inferred from the sole amino acid composition of a protein, residues located in hydrophobically unfavorable environments can be easily detected. Such residues turn out to be often directly involved in binding ligands or interfacing with other proteins.
|13.||Prymula K., Piwowar M., Kochańczyk M., Flis Ł., Malawski M., Szepieniec T., Evangelista G., Minervini G., Polticelli F., Wiśniowski Z., Sałapa K., Matczyńska E., Roterman I., In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature, CHEMISTRY AND BIODIVERSITY, ISSN: 1612-1872, DOI: 10.1002/cbdv.200800338, Vol.6, No.12, pp.2311-2336, 2009|
Prymula K., Piwowar M., Kochańczyk M.
, Flis Ł., Malawski M., Szepieniec T., Evangelista G., Minervini G., Polticelli F., Wiśniowski Z., Sałapa K., Matczyńska E., Roterman I., In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature
, CHEMISTRY AND BIODIVERSITY
, ISSN: 1612-1872
, DOI: 10.1002/cbdv.200800338
, Vol.6, No.12, pp.2311-2336, 2009
The three-dimensional structures of a set of ‘never born proteins’ (NBP, random amino acid sequence proteins with no significant homology with known proteins) were predicted using two methods: Rosetta and the one based on the ‘fuzzy-oil-drop’ (FOD) model. More than 3000 different random amino acid sequences have been generated, filtered against the non redundant protein sequence data base, to remove sequences with significant homology with known proteins, and subjected to three-dimensional structure prediction. Comparison between Rosetta and FOD predictions allowed to select the ten top (highest structural similarity) and the ten bottom (the lowest structural similarity) structures from the ranking list organized according to the RMS-D value. The selected structures were taken for detailed analysis to define the scale of structural accordance and discrepancy between the two methods. The structural similarity measurements revealed discrepancies between structures generated on the basis of the two methods. Their potential biological function appeared to be quite different as well. The ten bottom structures appeared to be ‘unfoldable’ for the FOD model. Some aspects of the general characteristics of the NBPs are also discussed. The calculations were performed on the EUChinaGRID grid platform to test the performance of this infrastructure for massive protein structure predictions.
|14.||Bryliński M., Kochańczyk M., Broniatowska E., Roterman I., Localization of ligand binding site in proteins identified in silico, Journal of Molecular Modeling, ISSN: 1610-2940, DOI: 10.1007/s00894-007-0191-x, Vol.13, No.6, pp.665-675, 2007|
Bryliński M., Kochańczyk M.
, Broniatowska E., Roterman I., Localization of ligand binding site in proteins identified in silico
, Journal of Molecular Modeling
, ISSN: 1610-2940
, DOI: 10.1007/s00894-007-0191-x
, Vol.13, No.6, pp.665-675, 2007
Knowledge-based models for protein folding assume that the early-stage structural form of a polypeptide is determined by the backbone conformation, followed by hydrophobic collapse. Side chain–side chain interactions, mostly of hydrophobic character, lead to the formation of the hydrophobic core, which seems to stabilize the structure of the protein in its natural environment. The fuzzy-oil-drop model is employed to represent the idealized hydrophobicity distribution in the protein molecule. Comparing it with the one empirically observed in the protein molecule reveals that they are not in agreement. It is shown in this study that the irregularity of hydrophobic distributions is aim-oriented. The character and strength of these irregularities in the organization of the hydrophobic core point to the specificity of a particular protein’s structure/function. When the location of these irregularities is determined versus the idealized fuzzy-oil-drop, function-related areas in the protein molecule can be identified. The presented model can also be used to identify ways in which protein–protein complexes can possibly be created. Active sites can be predicted for any protein structure according to the presented model with the free prediction server at http://www.bioinformatics.cm-uj.krakow.pl/activesite. The implication based on the model presented in this work suggests the necessity of active presence of ligand during the protein folding process simulation.
Hydrophobic collapse, Protein folding, Active site, Ligand binding
|15.||Bryliński M., Prymula K., Jurkowski W., Kochańczyk M., Stawowczyk E., Konieczny L., Roterman I., Prediction of Functional Sites Based on the Fuzzy Oil Drop Model, PLOS COMPUTATIONAL BIOLOGY, ISSN: 1553-734X, DOI: 10.1371/journal.pcbi.0030094, Vol.3, No.5, pp.e94-0909-0923, 2007|
Bryliński M., Prymula K., Jurkowski W., Kochańczyk M.
, Stawowczyk E., Konieczny L., Roterman I., Prediction of Functional Sites Based on the Fuzzy Oil Drop Model
, PLOS COMPUTATIONAL BIOLOGY
, ISSN: 1553-734X
, DOI: 10.1371/journal.pcbi.0030094
, Vol.3, No.5, pp.e94-0909-0923, 2007
A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localization of active sites in proteins. This paper describes a computational model that can be used to identify potential areas that are able to interact with other molecules (ligands, substrates, inhibitors, etc.). The model for active site recognition is based on the analysis of hydrophobicity distribution in protein molecules. It is shown, based on the analyses of proteins with known biological activity and of proteins of unknown function, that the region of significantly irregular hydrophobicity distribution in proteins appears to be function related.
Protein structure, Amino acid analysis, Isomerases, Protein structure prediction, Genomic databases, Structural genomics, Protein structure comparison, Oils
|16.||Bryliński M., Kochańczyk M., Konieczny L., Roterman I., Sequence-structure-function relation characterized in silico, In Silico Biology, ISSN: 1386-6338, Vol.6, No.6, pp.589-600, 2006|
Bryliński M., Kochańczyk M.
, Konieczny L., Roterman I., Sequence-structure-function relation characterized in silico
, In Silico Biology
, ISSN: 1386-6338
, Vol.6, No.6, pp.589-600, 2006
Hydrophobicity, biological function, active site, proteins of unknown biological function