dr Jan Ludwiczak

@article{https://doi.org/10.1002/pro.4846,

title = {AlphaFold2 captures the conformational landscape of the HAMP signaling domain},

author = {Aleksander Winski and Jan Ludwiczak and Malgorzata Orlowska and Rafal Madaj and Kamil Kaminski and Stanislaw Dunin-Horkawicz},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4846},

doi = {https://doi.org/10.1002/pro.4846},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Protein Science},

volume = {33},

number = {1},

pages = {e4846},

abstract = {Abstract In this study, we present a conformational landscape of 5000 AlphaFold2 models of the Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases (HAMP) domain, a short helical bundle that transduces signals from sensors to effectors in two-component signaling proteins such as sensory histidine kinases and chemoreceptors. The landscape reveals the conformational variability of the HAMP domain, including rotations, shifts, displacements, and tilts of helices, many combinations of which have not been observed in experimental structures. HAMP domains belonging to a single family tend to occupy a defined region of the landscape, even when their sequence similarity is low, suggesting that individual HAMP families have evolved to operate in a specific conformational range. The functional importance of this structural conservation is illustrated by poly-HAMP arrays, in which HAMP domains from families with opposite conformational preferences alternate, consistent with the rotational model of signal transduction. The only poly-HAMP arrays that violate this rule are predicted to be of recent evolutionary origin and structurally unstable. Finally, we identify a family of HAMP domains that are likely to be dynamic due to the presence of a conserved pi-helical bulge. All code associated with this work, including a tool for rapid sequence-based prediction of the rotational state in HAMP domains, is deposited at https://github.com/labstructbioinf/HAMPpred.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/bioinformatics/btad579b,

title = {pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models},

author = {Kamil Kaminski and Jan Ludwiczak and Kamil Pawlicki and Vikram Alva and Stanislaw Dunin-Horkawicz},

url = {https://doi.org/10.1093/bioinformatics/btad579},

doi = {10.1093/bioinformatics/btad579},

issn = {1367-4811},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Bioinformatics},

volume = {39},

number = {10},

pages = {btad579},

abstract = {The detection of homology through sequence comparison is a typical first step in the study of protein function and evolution. In this work, we explore the applicability of protein language models to this task.We introduce pLM-BLAST, a tool inspired by BLAST, that detects distant homology by comparing single-sequence representations (embeddings) derived from a protein language model, ProtT5. Our benchmarks reveal that pLM-BLAST maintains a level of accuracy on par with HHsearch for both highly similar sequences (with >50% identity) and markedly divergent sequences (with <30% identity), while being significantly faster. Additionally, pLM-BLAST stands out among other embedding-based tools due to its ability to compute local alignments. We show that these local alignments, produced by pLM-BLAST, often connect highly divergent proteins, thereby highlighting its potential to uncover previously undiscovered homologous relationships and improve protein annotation.pLM-BLAST is accessible via the MPI Bioinformatics Toolkit as a web server for searching precomputed databases (https://toolkit.tuebingen.mpg.de/tools/plmblast). It is also available as a standalone tool for building custom databases and performing batch searches (https://github.com/labstructbioinf/pLM-BLAST).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SDH2h,

title = {\textit{localpdb} —a Python package to manage protein structures and their annotations},

author = {Jan Ludwiczak and Aleksander Winski and Stanislaw Dunin-Horkawicz},

doi = {10.1093/bioinformatics/btac121},

issn = {1367-4803},

year  = {2022},

date = {2022-01-01},

journal = {Bioinformatics},

abstract = {The wealth of protein structures collected in the Protein Data Bank enabled large-scale studies of their

function and evolution. Such studies, however, require the generation of customized datasets combining the struc-

tural data with miscellaneous accessory resources providing functional, taxonomic and other annotations.

Unfortunately, the functionality of currently available tools for the creation of such datasets is limited and their usage

frequently requires laborious surveying of various data sources and resolving inconsistencies between their

versions.

To address this problem, we developed localpdb, a versatile Python library for the management of protein

structures and their annotations. The library features a flexible plugin system enabling seamless unification of the

structural data with diverse auxiliary resources, full version control and powerful functionality of creating highly cus-

tomized datasets. The localpdb can be used in a wide range of bioinformatic tasks, in particular those involving

large-scale protein structural analyses and machine learning.

Availability and implementation: localpdb is freely available at https://github.com/labstructbioinf/localpdb.

Documentation along with the usage examples can be accessed at https://labstructbioinf.github.io/localpdb/.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SDH5,

title = {Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins},

author = {Kamil Kamiński and Jan Ludwiczak and Maciej Jasiński and Adriana Bukala and Rafal Madaj and Krzysztof Szczepaniak and Stanisław Dunin-Horkawicz},

doi = {10.1093/bib/bbab371},

issn = {1467-5463},

year  = {2022},

date = {2022-01-01},

journal = {Briefings in Bioinformatics},

volume = {23},

abstract = {The Rossmann fold enzymes are involved in essential biochemical pathways such as nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors, small nucleoside-based compounds specifically recognized by a conserved βαβ motif shared by all Rossmann fold proteins. While Rossmann methyltransferases recognize only a single cofactor type, the S-adenosylmethionine, the oxidoreductases, depending on the family, bind nicotinamide (nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate) or flavin-based (flavin adenine dinucleotide) cofactors. In this study, we showed that despite its short length, the βαβ motif unambiguously defines the specificity towards the cofactor. Following this observation, we trained two complementary deep learning models for the prediction of the cofactor specificity based on the sequence and structural features of the βαβ motif. A benchmark on two independent test sets, one containing βαβ motifs bearing no resemblance to those of the training set, and the other comprising 38 experimentally confirmed cases of rational design of the cofactor specificity, revealed the nearly perfect performance of the two methods. The Rossmann-toolbox protocols can be accessed via the webserver at https://lbs.cent.uw.edu.pl/rossmann-toolbox and are available as a Python package at https://github.com/labstructbioinf/rossmann-toolbox.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SDH1,

title = {Siah-1-interacting protein regulates mutated huntingtin protein aggregation in Huntington’s disease models},

author = {Ewelina Latoszek and Małgorzata Wiweger and Jan Ludwiczak and Stanisław Dunin-Horkawicz and Jacek Kuznicki and Magdalena Czeredys},

doi = {10.1186/s13578-022-00755-0},

issn = {2045-3701},

year  = {2022},

date = {2022-01-01},

journal = {Cell & Bioscience},

volume = {12},

pages = {34},

abstract = {Background

Huntington’s disease (HD) is a neurodegenerative disorder whereby mutated huntingtin protein (mHTT) aggregates when polyglutamine repeats in the N-terminal of mHTT exceeds 36 glutamines (Q). However, the mechanism of this pathology is unknown. Siah1-interacting protein (SIP) acts as an adaptor protein in the ubiquitination complex and mediates degradation of other proteins. We hypothesized that mHTT aggregation depends on the dysregulation of SIP activity in this pathway in HD.



Results

A higher SIP dimer/monomer ratio was observed in the striatum in young YAC128 mice, which overexpress mHTT. We found that SIP interacted with HTT. In a cellular HD model, we found that wildtype SIP increased mHTT ubiquitination, attenuated mHTT protein levels, and decreased HTT aggregation. We predicted mutations that should stabilize SIP dimerization and found that SIP mutant-overexpressing cells formed more stable dimers and had lower activity in facilitating mHTT ubiquitination and preventing exon 1 mHTT aggregation compared with wildtype SIP.



Conclusions

Our data suggest that an increase in SIP dimerization in HD medium spiny neurons leads to a decrease in SIP function in the degradation of mHTT through a ubiquitin–proteasome pathway and consequently an increase in mHTT aggregation. Therefore, SIP could be considered a potential target for anti-HD therapy during the early stage of HD pathology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SDH7,

title = {A library of coiled-coil domains: from regular bundles to peculiar twists},

author = {Krzysztof Szczepaniak and Adriana Bukala and Antonio Marinho Silva da Neto and Jan Ludwiczak and Stanislaw Dunin-Horkawicz},

doi = {10.1093/bioinformatics/btaa1041},

issn = {1367-4803},

year  = {2021},

date = {2021-01-01},

journal = {Bioinformatics},

volume = {36},

pages = {5368-5376},

abstract = {Motivation



Coiled coils are widespread protein domains involved in diverse processes ranging from providing structural rigidity to the transduction of conformational changes. They comprise two or more α-helices that are wound around each other to form a regular supercoiled bundle. Owing to this regularity, coiled-coil structures can be described with parametric equations, thus enabling the numerical representation of their properties, such as the degree and handedness of supercoiling, rotational state of the helices, and the offset between them. These descriptors are invaluable in understanding the function of coiled coils and designing new structures of this type. The existing tools for such calculations require manual preparation of input and are therefore not suitable for the high-throughput analyses.



Results

To address this problem, we developed SamCC-Turbo, a software for fully automated, per-residue measurement of coiled coils. By surveying Protein Data Bank with SamCC-Turbo, we generated a comprehensive atlas of ∼50 000 coiled-coil regions. This machine learning-ready dataset features precise measurements as well as decomposes coiled-coil structures into fragments characterized by various degrees of supercoiling. The potential applications of SamCC-Turbo are exemplified by analyses in which we reveal general structural features of coiled coils involved in functions requiring conformational plasticity. Finally, we discuss further directions in the prediction and modeling of coiled coils.



Availability and implementation

SamCC-Turbo is available as a web server (https://lbs.cent.uw.edu.pl/samcc_turbo) and as a Python library (https://github.com/labstructbioinf/samcc_turbo), whereas the results of the Protein Data Bank scan can be browsed and downloaded at https://lbs.cent.uw.edu.pl/ccdb.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SDH6,

title = {Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins},

author = {M Adamczyk and E Lewicka and R Szatkowska and H Nieznanska and J Ludwiczak and M Jasiński and S Dunin-Horkawicz and E Sitkiewicz and B Swiderska and G Goch and G Jagura-Burdzy},

doi = {10.1186/s12866-020-02079-w},

issn = {1471-2180},

year  = {2021},

date = {2021-01-01},

journal = {BMC Microbiology},

volume = {21},

pages = {32},

abstract = {Background

DNA binding KfrA-type proteins of broad-host-range bacterial plasmids belonging to IncP-1 and IncU incompatibility groups are characterized by globular N-terminal head domains and long alpha-helical coiled-coil tails. They have been shown to act as transcriptional auto-regulators.



Results

This study was focused on two members of the growing family of KfrA-type proteins encoded by the broad-host-range plasmids, R751 of IncP-1β and RA3 of IncU groups. Comparative in vitro and in silico studies on KfrAR751 and KfrARA3 confirmed their similar biophysical properties despite low conservation of the amino acid sequences. They form a wide range of oligomeric forms in vitro and, in the presence of their cognate DNA binding sites, they polymerize into the higher order filaments visualized as “threads” by negative staining electron microscopy. The studies revealed also temperature-dependent changes in the coiled-coil segment of KfrA proteins that is involved in the stabilization of dimers required for DNA interactions.



Conclusion

KfrAR751 and KfrARA3 are structural homologues. We postulate that KfrA type proteins have moonlighting activity. They not only act as transcriptional auto-regulators but form cytoskeletal structures, which might facilitate plasmid DNA delivery and positioning in the cells before cell division, involving thermal energy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {β‐sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β‐amyloid fibrils},

author = {Adam Jarmuła and Jan Ludwiczak and Dariusz Stępkowski},

doi = {10.1002/prot.26057},

issn = {0887-3585},

year  = {2021},

date = {2021-01-01},

journal = {Proteins: Structure, Function, and Bioinformatics},

volume = {89},

pages = {762-780},

abstract = {β-sheet breakers (BSB) constitute a class of peptide inhibitors of amyloidogenesis, a process which is a hallmark of many diseases called amyloidoses, including Alzheimer's disease (AD); however, the molecular details of their action are still not fully understood. Here we describe the results of the computational investigation of the three BSBs, iaβ6 (LPFFFD), iaβ5 (LPFFD), and iaβ6_Gly (LPFGFD), in complex with the fibril model of Aβ42 and propose the kinetically probable mechanism of their action. The mechanism involves the binding of BSB to the central hydrophobic core (CHC) region (LVFFA) of Aβ fibril and the π-stacking of its Phe rings both internally and with the Aβ fibril. In the process, the Aβ fibril undergoes distortion accumulating on the side of chain A (located on the odd tip of the fibril). In a single replica of extended molecular dynamics run of one of the iaβ6 poses, the distortion concludes in a dissociation of chain A from the fibril model of Aβ42. Altogether, we postulate that including consecutive Phe residues into BSBs docked around Phe 20 in the CHC region of Aβ42 improve their potency for dissolution of fibrils. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SDH8,

title = {C8J_1298, a bifunctional thiol oxidoreductase of Campylobacter jejuni, affects Dsb (disulfide bond) network functioning},

author = {Anna Marta Banaś and Katarzyna Marta Bocian-Ostrzycka and Maciej Plichta and Stanisław Dunin-Horkawicz and Jan Ludwiczak and Jagoda Płaczkiewicz and Elżbieta Katarzyna Jagusztyn-Krynicka},

doi = {10.1371/journal.pone.0230366},

issn = {1932-6203},

year  = {2020},

date = {2020-01-01},

journal = {PLOS ONE},

volume = {15},

pages = {e0230366},

abstract = {Posttranslational generation of disulfide bonds catalyzed by bacterial Dsb (disulfide bond) enzymes is essential for the oxidative folding of many proteins. Although we now have a good understanding of the Escherichia coli disulfide bond formation system, there are significant gaps in our knowledge concerning the Dsb systems of other bacteria, including Campylobacter jejuni, a food-borne, zoonotic pathogen. We attempted to gain a more complete understanding of the process by thorough analysis of C8J_1298 functioning in vitro and in vivo. C8J_1298 is a homodimeric thiol-oxidoreductase present in wild type (wt) cells, in both reduced and oxidized forms. The protein was previously described as a homolog of DsbC, and thus potentially should be active in rearrangement of disulfides. Indeed, biochemical studies with purified protein revealed that C8J_1298 shares many properties with EcDsbC. However, its activity in vivo is dependent on the genetic background, namely, the set of other Dsb proteins present in the periplasm that determine the redox conditions. In wt C. jejuni cells, C8J_1298 potentially works as a DsbG involved in the control of the cysteine sulfenylation level and protecting single cysteine residues from oxidation to sulfenic acid. A strain lacking only C8J_1298 is indistinguishable from the wild type strain by several assays recognized as the criteria to determine isomerization or oxidative Dsb pathways. Remarkably, in C. jejuni strain lacking DsbA1, the protein involved in generation of disulfides, C8J_1298 acts as an oxidase, similar to the homodimeric oxidoreductase of Helicobater pylori, HP0231. In E. coli, C8J_1298 acts as a bifunctional protein, also resembling HP0231. These findings are strongly supported by phylogenetic data. We also showed that CjDsbD (C8J_0565) is a C8J_1298 redox partner.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SDH11,

title = {DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences},

author = {Jan Ludwiczak and Aleksander Winski and Krzysztof Szczepaniak and Vikram Alva and Stanislaw Dunin-Horkawicz},

doi = {10.1093/bioinformatics/bty1062},

issn = {1367-4803},

year  = {2019},

date = {2019-01-01},

journal = {Bioinformatics},

volume = {35},

pages = {2790-2795},

abstract = {Motivation

Coiled coils are protein structural domains that mediate a plethora of biological interactions, and thus their reliable annotation is crucial for studies of protein structure and function.



Results

Here, we report DeepCoil, a new neural network-based tool for the detection of coiled-coil domains in protein sequences. In our benchmarks, DeepCoil significantly outperformed current state-of-the-art tools, such as PCOILS and Marcoil, both in the prediction of canonical and non-canonical coiled coils. Furthermore, in a scan of the human genome with DeepCoil, we detected many coiled-coil domains that remained undetected by other methods. This higher sensitivity of DeepCoil should make it a method of choice for accurate genome-wide detection of coiled-coil domains.



Availability and implementation

DeepCoil is written in Python and utilizes the Keras machine learning library. A web server is freely available at https://toolkit.tuebingen.mpg.de/#/tools/deepcoil and a standalone version can be downloaded at https://github.com/labstructbioinf/DeepCoil.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ludwiczak2019,

title = {Interactions between motor domains in kinesin-14 Ncd — a molecular dynamics study},

author = {Jan Ludwiczak and Ewa Szczęsna and Antônio Marinho Silva da Neto and Piotr Cieplak and Andrzej A Kasprzak and Adam Jarmuła},

doi = {10.1042/BCJ20190484},

issn = {0264-6021},

year  = {2019},

date = {2019-01-01},

journal = {Biochemical Journal},

volume = {476},

pages = {2449-2462},

abstract = {Minus-end directed, non-processive kinesin-14 Ncd is a dimeric protein with C-terminally located motor domains (heads). Generation of the power-stroke by Ncd consists of a lever-like rotation of a long superhelical ‘stalk’ segment while one of the kinesin's heads is bound to the microtubule. The last ∼30 amino acids of Ncd head play a crucial but still poorly understood role in this process. Here, we used accelerated molecular dynamics simulations to explore the conformational dynamics of several systems built upon two crystal structures of Ncd, the asymmetrical T436S mutant in pre-stroke/post-stroke conformations of two partner subunits and the symmetrical wild-type protein in pre-stroke conformation of both subunits. The results revealed a new conformational state forming following the inward motion of the subunits and stabilized with several hydrogen bonds to residues located on the border or within the C-terminal linker, i.e. a modeled extension of the C-terminus by residues 675–683. Forming of this new, compact Ncd conformation critically depends on the length of the C-terminus extending to at least residue 681. Moreover, the associative motion leading to the compact conformation is accompanied by a partial lateral rotation of the stalk. We propose that the stable compact conformation of Ncd may represent an initial state of the working stroke.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ludwiczak2019b,

title = {PiPred – a deep-learning method for prediction of π-helices in protein sequences},

author = {Jan Ludwiczak and Aleksander Winski and Antonio Marinho Silva da Neto and Krzysztof Szczepaniak and Vikram Alva and Stanislaw Dunin-Horkawicz},

doi = {10.1038/s41598-019-43189-4},

issn = {2045-2322},

year  = {2019},

date = {2019-01-01},

journal = {Scientific Reports},

volume = {9},

pages = {6888},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SDH13,

title = {Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design},

author = {Jan Ludwiczak and Adam Jarmula and Stanislaw Dunin-Horkawicz},

doi = {10.1016/j.jsb.2018.02.004},

issn = {10478477},

year  = {2018},

date = {2018-01-01},

journal = {Journal of Structural Biology},

volume = {203},

pages = {54-61},

abstract = {Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20–30% more diverse sequences than currently available methods with only a slight increase in computation time. Importantly, the increase in diversity is achieved without a loss in the quality of the designed sequences assessed by their resemblance to natural sequences. We demonstrate that the MD-based procedure is also applicable to de novo design tasks started from backbone structures without any sequence information. In addition, we implemented a protocol that can be used to assess the stability of designed models and to select the best candidates for experimental validation. In sum our results demonstrate that the MD ensemble-based flexible backbone design can be a viable method for protein design, especially for tasks that require a large pool of diverse sequences.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Szczepaniak2018,

title = {Variability of the core geometry in parallel coiled-coil bundles},

author = {Krzysztof Szczepaniak and Jan Ludwiczak and Aleksander Winski and Stanislaw Dunin-Horkawicz},

doi = {10.1016/j.jsb.2018.07.002},

issn = {10478477},

year  = {2018},

date = {2018-01-01},

journal = {Journal of Structural Biology},

volume = {204},

pages = {117-124},

abstract = {In protein modelling and design, an understanding of the relationship between sequence and structure is essential. Using parallel, homotetrameric coiled-coil structures as a model system, we demonstrated that machine learning techniques can be used to predict structural parameters directly from the sequence. Coiled coils are regular protein structures, which are of great interest as building blocks for assembling larger nanostructures. They are composed of two or more alpha-helices wrapped around each other to form a supercoiled bundle. The coiled-coil bundles are defined by four basic structural parameters: topology (parallel or antiparallel), radius, degree of supercoiling, and the rotation of helices around their axes. In parallel coiled coils the latter parameter, describing the hydrophobic core packing geometry, was assumed to show little variation. However, we found that subtle differences between structures of this type were not artifacts of structure determination and could be predicted directly from the sequence. Using this information in modelling narrows the structural parameter space that must be searched and thus significantly reduces the required computational time. Moreover, the sequence-structure rules can be used to explain the effects of point mutations and to shed light on the relationship between hydrophobic core architecture and coiled-coil topology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Crystal structures of nematode (parasitic T. spiralis and free living C. elegans ), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS},

author = {Adam Jarmuła and Piotr Wilk and Piotr Maj and Jan Ludwiczak and Anna Dowierciał and Katarzyna Banaszak and Wojciech Rypniewski and Joanna Cieśla and Magdalena Dąbrowska and Tomasz Frączyk and Agnieszka K Bronowska and Jakub Jakowiecki and Sławomir Filipek and Wojciech Rode},

doi = {10.1016/j.jmgm.2017.08.008},

issn = {10933263},

year  = {2017},

date = {2017-01-01},

journal = {Journal of Molecular Graphics and Modelling},

volume = {77},

pages = {33-50},

abstract = {Three crystal structures are presented of nematode thymidylate synthases (TS), including Caenorhabditis elegans (Ce) enzyme without ligands and its ternary complex with dUMP and Raltitrexed, and binary complex of Trichinella spiralis (Ts) enzyme with dUMP. In search of differences potentially relevant for the development of species-specific inhibitors of the nematode enzyme, a comparison was made of the present Ce and Ts enzyme structures, as well as binary complex of Ce enzyme with dUMP, with the corresponding mammalian (human, mouse and rat) enzyme crystal structures. To complement the comparison, tCONCOORD computations were performed to evaluate dynamic behaviors of mammalian and nematode TS structures. Finally, comparative molecular docking combined with molecular dynamics and free energy of binding calculations were carried out to search for ligands showing selective affinity to T. spiralis TS. Despite an overall strong similarity in structure and dynamics of nematode vs mammalian TSs, a pool of ligands demonstrating predictively a strong and selective binding to TsTS has been delimited. These compounds, the E63 family, locate in the dimerization interface of TsTS where they exert species-specific interactions with certain non-conserved residues, including hydrogen bonds with Thr174 and hydrophobic contacts with Phe192, Cys191 and Tyr152. The E63 family of ligands opens the possibility of future development of selective inhibitors of TsTS and effective agents against trichinellosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ludwiczak2016,

title = {Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N ^{4} -hydroxy-dCMP},

author = {Jan Ludwiczak and Piotr Maj and Piotr Wilk and Tomasz Frączyk and Tomasz Ruman and Borys Kierdaszuk and Adam Jarmuła and Wojciech Rode},

doi = {10.1039/C6MB00026F},

issn = {1742-206X},

year  = {2016},

date = {2016-01-01},

journal = {Molecular BioSystems},

volume = {12},

pages = {1333-1341},

abstract = {Endogenous thymidylate synthases, isolated from tissues or cultured cells of the same specific origin, have been reported to show differing slow-binding inhibition patterns. These were reflected by biphasic or linear dependence of the inactivation rate on time and accompanied by differing inhibition parameters. Considering its importance for chemotherapeutic drug resistance, the possible effect of thymidylate synthase inhibition by post-translational modification was tested, e.g. phosphorylation, by comparing sensitivities to inhibition by two slow-binding inhibitors, 5-fluoro-dUMP and N4-hydroxy-dCMP, of two fractions of purified recombinant mouse enzyme preparations, phosphorylated and non-phosphorylated, separated by metal oxide/hydroxide affinity chromatography on Al(OH)3 beads. The modification, found to concern histidine residues and influence kinetic properties by lowering Vmax, altered both the pattern of dependence of the inactivation rate on time from linear to biphasic, as well as slow-binding inhibition parameters, with each inhibitor studied. Being present on only one subunit of at least a great majority of phosphorylated enzyme molecules, it probably introduced dimer asymmetry, causing the altered time dependence of the inactivation rate pattern (biphasic with the phosphorylated enzyme) and resulting in asymmetric binding of each inhibitor studied. The latter is reflected by the ternary complexes, stable under denaturing conditions, formed by only the non-phosphorylated subunit of the phosphorylated enzyme with each of the two inhibitors and N5,10-methylenetetrahydrofolate. Inhibition of the phosphorylated enzyme by N4-hydroxy-dCMP was found to be strongly dependent on [Mg2+], cations demonstrated previously to also influence the activity of endogenous mouse TS isolated from tumour cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}