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Engström, Åke
Alternative names
Publications (10 of 53) Show all publications
Liu, Y., Zhang, D., Engström, Å., Merenyi, G., Hagner, M., Yang, H., . . . Sjolinder, H. (2016). Dynamic niche-specific adaptations in Neisseria meningitidis during infection. Microbes and infection, 18(2), 109-117
Open this publication in new window or tab >>Dynamic niche-specific adaptations in Neisseria meningitidis during infection
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2016 (English)In: Microbes and infection, ISSN 1286-4579, E-ISSN 1769-714X, Vol. 18, no 2, p. 109-117Article in journal (Refereed) Published
Abstract [en]

Neisseria meningitidis is an opportunistic human pathogen that usually colonizes the nasopharyngeal mucosa asymptomatically. Upon invasion into the blood and central nervous system, this bacterium triggers a fulminant inflammatory reaction with the manifestations of septicemia and meningitis, causing high morbidity and mortality. To reveal the bacterial adaptations to specific and dynamic host environments, we performed a comprehensive proteomic survey of N. meningitidis isolated from the nasal mucosa, CSF and blood of a mouse disease model. We could identify 51 proteins whose expression pattern has been changed during infection, many of which have not yet been characterized. The abundance of proteins was markedly lower in the bacteria isolated from the nasal mucosa compared to the bacteria from the blood and CSF, indicating that initiating adhesion is the harshest challenge for meningococci. The high abundance of the glutamate dehydrogenase (GdhA) and Opa1800 proteins in all bacterial isolates suggests their essential role in bacterial survival in vivo. To evaluate the biological relevance of our proteomic findings, four candidate proteins from representative functional groups, such as the bacterial chaperone GroEL, IMP dehydrogenase GuaB, and membrane proteins PilQ and NMC0101, were selected and their impact on bacterial fitness was investigated by mutagenesis assays. This study provides an integrated picture of bacterial niche-specific adaptations during consecutive infection processes.

Keyword
Neisseria meningitidis, Host adaptation, Virulence, Proteomic analysis
National Category
Infectious Medicine Immunology in the medical area
Identifiers
urn:nbn:se:uu:diva-281966 (URN)10.1016/j.micinf.2015.09.025 (DOI)000370375400005 ()26482500 (PubMedID)
Funder
Swedish Research Council, 2008-2572Swedish Research Council, 2008-3367
Available from: 2016-04-01 Created: 2016-04-01 Last updated: 2018-01-10Bibliographically approved
Karlsson, O. A., Ramirez, J., Öberg, D., Malmqvist, T., Engström, Å., Friberg, M., . . . Jemth, P. (2015). Design of a PDZbody, a bivalent binder of the E6 protein from human papillomavirus. Scientific Reports, 5, Article ID 9382.
Open this publication in new window or tab >>Design of a PDZbody, a bivalent binder of the E6 protein from human papillomavirus
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2015 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 9382Article in journal (Refereed) Published
Abstract [en]

Chronic infection by high risk human papillomavirus (HPV) strains may lead to cancer. Expression of the two viral oncoproteins E6 and E7 is largely responsible for immortalization of infected cells. The HPV E6 is a small (approximately 150 residues) two domain protein that interacts with a number of cellular proteins including the ubiquitin ligase E6-associated protein (E6AP) and several PDZ-domain containing proteins. Our aim was to design a high-affinity binder for HPV E6 by linking two of its cellular targets. First, we improved the affinity of the second PDZ domain from SAP97 for the C-terminus of HPV E6 from the high-risk strain HPV18 using phage display. Second, we added a helix from E6AP to the N-terminus of the optimized PDZ variant, creating a chimeric bivalent binder, denoted PDZbody. Full-length HPV E6 proteins are difficult to express and purify. Nevertheless, we could measure the affinity of the PDZbody for E6 from another high-risk strain, HPV16 (K-d = 65 nM). Finally, the PDZbody was used to co-immunoprecipitate E6 protein from HPV18-immortalized HeLa cells, confirming the interaction between PDZbody and HPV18 E6 in a cellular context.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-258849 (URN)10.1038/srep09382 (DOI)000351373500005 ()25797137 (PubMedID)
Funder
Swedish Cancer Society
Available from: 2015-07-23 Created: 2015-07-20 Last updated: 2017-12-04Bibliographically approved
Jemth, P., Mu, X., Engström, Å. & Dogan, J. (2014). A Frustrated Binding Interface for Intrinsically Disordered Proteins. Journal of Biological Chemistry, 289(9), 5528-5533
Open this publication in new window or tab >>A Frustrated Binding Interface for Intrinsically Disordered Proteins
2014 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 289, no 9, p. 5528-5533Article in journal (Refereed) Published
Abstract [en]

Background: Protein-protein interactions often involve intrinsically disordered protein domains. Results: The binding interface between two disordered protein domains is suboptimal, or frustrated, with regard to the energetics. Conclusion: The frustration likely results from the promiscuous binding behavior of these disordered domains. Significance: Suboptimal binding interfaces may be common among intrinsically disordered proteins with multiple binding partners. Intrinsically disordered proteins are very common in the eukaryotic proteome, and many of them are associated with diseases. Disordered proteins usually undergo a coupled binding and folding reaction and often interact with many different binding partners. Using double mutant cycles, we mapped the energy landscape of the binding interface for two interacting disordered domains and found it to be largely suboptimal in terms of interaction free energies, despite relatively high affinity. These data depict a frustrated energy landscape for interactions involving intrinsically disordered proteins, which is likely a result of their functional promiscuity.

Keyword
Intrinsically Disordered Proteins, Kinetics, Protein Domains, Protein Engineering, Protein-Protein Interactions
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-227573 (URN)10.1074/jbc.M113.537068 (DOI)000332015500017 ()
Available from: 2014-06-30 Created: 2014-06-27 Last updated: 2017-12-05Bibliographically approved
Hultqvist, G., Haq, R., Punekar, A., Chi, C., Engström, Å., Bach, A., . . . Jemth, P. (2013). Energetic pathway sampling in a protein interaction domain. Structure, 21, 1193-1202
Open this publication in new window or tab >>Energetic pathway sampling in a protein interaction domain
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2013 (English)In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 21, p. 1193-1202Article in journal (Other academic) Published
Abstract [en]

The affinity and specificity of protein-ligand interactions are influenced by energeticcrosstalk within the protein domain. However, the molecular details of such intradomain allostery are still unclear. Here, we have experimentally detected and computationally predicted interactionpathways in the postsynaptic density 95/discs large/zonula occludens 1 (PDZ)-peptide ligand model system using wild-type and circularly permuted PDZ proteins. The circular permutant introduced small perturbations in the tertiary structure and a concomitant rewiring of allosteric pathways, allowing us to describe how subtle changes may reshape energetic signaling. The results were analyzed in the context of other members of the PDZ family, which were found to contain distinct interaction pathways for different peptide ligands. The data reveal a fascinating scenario whereby several energetic pathways are sampled within one single domain and distinct pathways are activated by specific protein ligands. 

Keyword
intradomain allostery, PDZ domain, protein binding, circular permutant
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:uu:diva-185579 (URN)10.1016/j.str.2013.05.010 (DOI)000321681600016 ()
Available from: 2012-12-10 Created: 2012-11-26 Last updated: 2017-10-16Bibliographically approved
Momeni, M. H., Payne, C. M., Hansson, H., Mikkelsen, N. E., Svedberg, J., Engström, Å., . . . Stahlberg, J. (2013). Structural, Biochemical, and Computational Characterization of the Glycoside Hydrolase Family 7 Cellobiohydrolase of the Tree-killing Fungus Heterobasidion irregulare. Journal of Biological Chemistry, 288(8), 5861-5872
Open this publication in new window or tab >>Structural, Biochemical, and Computational Characterization of the Glycoside Hydrolase Family 7 Cellobiohydrolase of the Tree-killing Fungus Heterobasidion irregulare
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2013 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 288, no 8, p. 5861-5872Article in journal (Refereed) Published
Abstract [en]

Root rot fungi of the Heterobasidion annosum complex are the most damaging pathogens in temperate forests, and the recently sequenced Heterobasidion irregulare genome revealed over 280 carbohydrate-active enzymes. Here, H. irregulare was grown on biomass, and the most abundant protein in the culture filtrate was identified as the only family 7 glycoside hydrolase in the genome, which consists of a single catalytic domain, lacking a linker and carbohydrate-binding module. The enzyme, HirCel7A, was characterized biochemically to determine the optimal conditions for activity. HirCel7A was crystallized and the structure, refined at 1.7 angstrom resolution, confirms that HirCel7A is a cellobiohydrolase rather than an endoglucanase, with a cellulose-binding tunnel that is more closed than Phanerochaete chrysosporium Cel7D and more open than Hypocrea jecorina Cel7A, suggesting intermediate enzyme properties. Molecular simulations were conducted to ascertain differences in enzyme-ligand interactions, ligand solvation, and loop flexibility between the family 7 glycoside hydrolase cellobiohydrolases from H. irregulare, H. jecorina, and P. chrysosporium. The structural comparisons and simulations suggest significant differences in enzyme-ligand interactions at the tunnel entrance in the -7 to -4 binding sites and suggest that a tyrosine residue at the tunnel entrance of HirCel7A may serve as an additional ligand-binding site. Additionally, the loops over the active site in H. jecorina Cel7A are more closed than loops in the other two enzymes, which has implications for the degree of processivity, endo- initiation, and substrate dissociation. Overall, this study highlights molecular level features important to understanding this biologically and industrially important family of glycoside hydrolases.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-197654 (URN)10.1074/jbc.M112.440891 (DOI)000315342500056 ()
Note

De två första författarna delar förstaförfattarskapet.

Available from: 2013-04-02 Created: 2013-04-02 Last updated: 2017-12-06Bibliographically approved
Dogan, J., Mu, X., Engström, Å. & Jemth, P. (2013). The transition state structure for coupled binding and folding of disordered protein domains. Scientific Reports, 3, 2076
Open this publication in new window or tab >>The transition state structure for coupled binding and folding of disordered protein domains
2013 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, p. 2076-Article in journal (Refereed) Published
Abstract [en]

Intrinsically disordered proteins are abundant in the eukaryotic proteome, and they are implicated in a range of different diseases. However, there is a paucity of experimental data on molecular details of the coupled binding and folding of such proteins. Two interacting and relatively well studied disordered protein domains are the activation domain from the p160 transcriptional co-activator ACTR and the nuclear co-activator binding domain (NCBD) of CREB binding protein. We have analyzed the transition state for their coupled binding and folding by protein engineering and kinetic experiments (Phi-value analysis) and found that it involves weak native interactions between the N-terminal helices of ACTR and NCBD, but is otherwise "disordered-like". Most native hydrophobic interactions in the interface between the two domains form later, after the rate-limiting barrier for association. Linear free energy relationships suggest a cooperative formation of native interactions, reminiscent of the nucleation-condensation mechanism in protein folding.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-204799 (URN)10.1038/srep02076 (DOI)000320847200012 ()
Available from: 2013-08-15 Created: 2013-08-12 Last updated: 2017-12-06Bibliographically approved
Dogan, J., Schmidt, T., Mu, X., Engström, Å. & Jemth, P. (2012). Fast Association and Slow Transitions in the Interaction between Two Intrinsically Disordered Protein Domains. Journal of Biological Chemistry, 287(41), 34316-34324
Open this publication in new window or tab >>Fast Association and Slow Transitions in the Interaction between Two Intrinsically Disordered Protein Domains
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2012 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 287, no 41, p. 34316-34324Article in journal (Refereed) Published
Abstract [en]

Proteins that contain long disordered regions are prevalent in the proteome and frequently associated with diseases. However, the mechanisms by which such intrinsically disordered proteins (IDPs) recognize their targets are not well understood. Here, we report the first experimental investigation of the interaction kinetics of the nuclear co-activator binding domain of CREB-binding protein and the activation domain from the p160 transcriptional co-activator for thyroid hormone and retinoid receptors. Both protein domains are intrinsically disordered in the free state and synergistically fold upon binding each other. Using the stopped-flow technique, we found that the binding reaction is fast, with an association rate constant of 3 x 10(7) M-1 s(-1) at 277 K. Mutation of a conserved buried intermolecular salt bridge showed that electrostatics govern the rapid association. Furthermore, upon mutation of the salt bridge or at high salt concentration, an additional kinetic phase was detected (similar to 20 and similar to 40 s(-1), respectively, at 277 K), suggesting that the salt bridge may steer formation of the productive bimolecular complex in an intramolecular step. Finally, we directly measured slow kinetics for the IDP domains (similar to 1 s(-1) at 277 K) related to conformational transitions upon binding. Together, the experiments demonstrate that the interaction involves several steps and accumulation of intermediate states. Our data are consistent with an induced fit mechanism, in agreement with previous simulations. We propose that the slow transitions may be a consequence of the multipartner interactions of IDPs.

Keyword
Coactivator Binding Domain, Conformational Selection, Unstructured Proteins, Complex, Cbp, Recruitment, Recognition, Mechanism, State
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-185193 (URN)10.1074/jbc.M112.399436 (DOI)000309654200035 ()
Available from: 2012-11-22 Created: 2012-11-21 Last updated: 2017-12-07Bibliographically approved
Chi, C. N., Haq, S. R., Rinaldo, S., Dogan, J., Cutruzzolà, F., Engström, Å., . . . Jemth, P. (2012). Interactions outside the boundaries of the canonical binding groove of a pdz domain influence ligand binding. Biochemistry, 51(44), 8971-8979
Open this publication in new window or tab >>Interactions outside the boundaries of the canonical binding groove of a pdz domain influence ligand binding
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2012 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 51, no 44, p. 8971-8979Article in journal (Refereed) Published
Abstract [en]

The postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ) domain is a protein-protein interaction module with a shallow binding groove where protein ligands bind. However, interactions that are not part of this canonical binding groove are likely to modulate peptide binding. We have investigated such interactions beyond the binding groove for PDZ3 from PSD-95 and a peptide derived from the C-terminus of the natural ligand CRIPT. We found via nuclear magnetic resonance experiments that up to eight residues of the peptide ligand interact with the PDZ domain, showing that the interaction surface extends far outside of the binding groove as defined by the crystal structure. PDZ3 contains an extra structural element, a C-terminal helix (α3), which is known to affect affinity. Deletion of this helix resulted in the loss of several intermolecular nuclear Overhauser enhancements from peptide residues outside of the binding pocket, suggesting that α3 forms part of the extra binding surface in wild-type PDZ3. Site-directed mutagenesis, isothermal titration calorimetry, and fluorescence intensity experiments confirmed the importance of both α3 and the N-terminal part of the peptide for the affinity. Our data suggest a general mechanism in which different binding surfaces outside of the PDZ binding groove could provide sites for specific interactions.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-186213 (URN)10.1021/bi300792h (DOI)000310664200025 ()
Available from: 2012-11-29 Created: 2012-11-28 Last updated: 2017-10-16Bibliographically approved
Haq, S. R., Chi, C. N., Bach, A., Dogan, J., Engström, Å., Hultqvist, G., . . . Jemth, P. (2012). Side-Chain Interactions Form Late and Cooperatively in the Binding Reaction between Disordered Peptides and PDZ Domains. Journal of the American Chemical Society, 134(1), 599-605
Open this publication in new window or tab >>Side-Chain Interactions Form Late and Cooperatively in the Binding Reaction between Disordered Peptides and PDZ Domains
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2012 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, no 1, p. 599-605Article in journal (Refereed) Published
Abstract [en]

Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. Here we have used short peptides as a model system for intrinsically disordered proteins. Linear free energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate-limiting barrier for binding and in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins toward their targets are generally governed by their association rate constants. Instead, we observed the opposite for peptide-PDZ interactions, namely, that changes in K-d correlate with changes in k(off).

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-172158 (URN)10.1021/ja209341w (DOI)000301084200096 ()
Available from: 2012-04-03 Created: 2012-04-02 Last updated: 2017-12-07Bibliographically approved
Karlsson, O. A., Chi, C. N., Engström, Å. & Jemth, P. (2012). The Transition State of Coupled Folding and Binding for a Flexible beta-Finger. Journal of Molecular Biology, 417(3), 253-261
Open this publication in new window or tab >>The Transition State of Coupled Folding and Binding for a Flexible beta-Finger
2012 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 417, no 3, p. 253-261Article in journal (Refereed) Published
Abstract [en]

Flexible and fully disordered protein regions that fold upon binding mediate numerous protein protein interactions. However, little is known about their mechanism of interaction. One such coupled folding and binding occurs when a flexible region of neuronal nitric oxide synthase adopts a beta-finger structure upon binding to its protein ligand, a PDZ [PSD-95 (postsynaptic density protein-95)/Discs large/ZO-1] domain from PSD-95. We have analyzed this binding reaction by protein engineering combined with kinetic experiments. Mutational destabilization of the beta-finger changed mainly the dissociation rate constant of the proteins and, to a lesser extent, the association rate constant. Thus, mutation affected late events in the coupled folding and binding reaction. Our results therefore suggest that the native binding interactions of the beta-finger are not present in the rate-limiting transition state for binding but form on the downhill side in a cooperative manner. However, by mutation, we could destabilize the beta-finger further and change the rate-limiting step such that an initial conformational change becomes rate limiting. This switch in rate-limiting step shows that multistep binding mechanisms are likely to be found among flexible and intrinsically disordered regions of proteins.

Keyword
intrinsically disordered proteins, PDZ domain, binding kinetics, phi binding, flexible proteins
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-172818 (URN)10.1016/j.jmb.2012.01.042 (DOI)000301805800010 ()
Available from: 2012-04-17 Created: 2012-04-16 Last updated: 2017-10-16Bibliographically approved
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