Structural Proteomics

New insights into complex formation by SARS-CoV-2 nsp10 and nsp14.

Sele C, Krupinska E, Andersson Rasmussen A, ..., Fisher SZ, Knecht W

Nucleosides Nucleotides Nucleic Acids - (-) 1-15 [2024-02-29; online 2024-02-29]

Multi-Modal Mass Spectrometry Identifies a Conserved Protective Epitope inS. pyogenesStreptolysin O

Year 2023

DOI Crossref

Tang D, Gueto-Tettay C, Hjortswang E, ..., Malmström L, Malmström J

- - (-) - [2023-12-02; online 2023-12-02]

Molecular view of ER membrane remodeling by the Sec61/TRAP translocon.

Karki S, Javanainen M, Rehan S, ..., Happonen L, Paavilainen V

EMBO Rep. - (-) e57910 [2023-11-20; online 2023-11-20]

Dissecting the properties of circulating IgG against Group A Streptococcus through a combined systems antigenomics-serology workflow

DOI Crossref

Chowdhury S, Gomez Toledo A, Hjortswang E, ..., Rasmussen M, Malmström J

- - (-) - [2023-11-09; online 2023-11-09]

The intracellular helical bundle of human glucose transporter GLUT4 is important for complex formation with ASPL.

Huang P, Åbacka H, Varela D, ..., André I, Lindkvist-Petersson K

FEBS Open Bio 13 (11) 2094-2107 [2023-11-00; online 2023-09-28]

Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs.

Petruk G, Puthia M, Samsudin F, ..., Lindstedt S, Schmidtchen A

Nat Commun 14 (1) 6097 [2023-09-29; online 2023-09-29]

Clinical Genomics Lund [Service] Structural Proteomics [Collaborative]

DOI Crossref

Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site

Bimaï O, Banerjee I, Grinberg IR, ..., Sjöberg BM, Logan DT

- - (-) - [2023-08-16; online 2023-08-16]

Cryo-EM [Service] Structural Proteomics [Service]

Reduced binding of apoE4 to complement factor H promotes amyloid-β oligomerization and neuroinflammation.

Chernyaeva L, Ratti G, Teirilä L, ..., Nissilä E, Haapasalo K

EMBO Rep. - (-) e56467 [2023-05-08; online 2023-05-08]

Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses.

Pushparaj P, Nicoletto A, Dopico XC, ..., Corcoran M, Karlsson Hedestam GB

Front Virol 3 (-) 1128253 [2023-03-01; online 2023-04-13]

A human monoclonal antibody bivalently binding two different epitopes in streptococcal M protein mediates immune function.

Bahnan W, Happonen L, Khakzad H, ..., Malmström J, Nordenfelt P

EMBO Mol Med 15 (2) e16208 [2023-02-08; online 2022-12-12]

Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies.

Pushparaj P, Nicoletto A, Sheward DJ, ..., Corcoran M, Karlsson Hedestam GB

Immunity 56 (1) 193-206.e7 [2023-01-10; online 2022-12-12]

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics.

Gueto-Tettay C, Tang D, Happonen L, ..., Malmström J, Malmström L

PLoS Comput. Biol. 19 (1) e1010457 [2023-01-00; online 2023-01-20]

Affinity-Purification Combined with Crosslinking Mass Spectrometry for Identification and Structural Modeling of Host–Pathogen Protein–Protein Complexes

Happonen LJ

Methods Mol. Biol. 2674 (-) 181-200 [2023-00-00; online 2023-06-01]

Year 2022

Snapshots of actin and tubulin folding inside the TRiC chaperonin.

Kelly JJ, Tranter D, Pardon E, ..., Huiskonen JT, Yue WW

Nat. Struct. Mol. Biol. - (-) - [2022-04-21; online 2022-04-21]

Interaction of Bartonella henselae with Fibronectin Represents the Molecular Basis for Adhesion to Host Cells.

Vaca DJ, Thibau A, Leisegang MS, ..., Happonen L, Kempf VAJ

Microbiol Spectr - (-) e0059822 [2022-04-18; online 2022-04-18]

Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies.

Hanke L, Sheward DJ, Pankow A, ..., McInerney GM, Murrell B

Sci Adv 8 (12) eabm0220 [2022-03-25; online 2022-03-25]

Pseudouridine-modified tRNA fragments repress aberrant protein synthesis and predict leukaemic progression in myelodysplastic syndrome.

Guzzi N, Muthukumar S, Cieśla M, ..., Dimitriou M, Bellodi C

Nat Cell Biol 24 (3) 299-306 [2022-03-00; online 2022-03-15]

Year 2021

Structural basis for transthyretin amyloid formation in vitreous body of the eye.

Iakovleva I, Hall M, Oelker M, ..., Anan I, Sauer-Eriksson AE

Nat Commun 12 (1) 7141 [2021-12-08; online 2021-12-08]

Cryo-EM [Collaborative] Structural Proteomics [Service]

Streptococcus pyogenes Forms Serotype- and Local Environment-Dependent Interspecies Protein Complexes.

Chowdhury S, Khakzad H, Bergdahl GE, ..., Happonen L, Malmström J

mSystems 6 (5) e0027121 [2021-10-26; online 2021-09-28]

(p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains.

Roghanian M, Van Nerom K, Takada H, ..., Garcia-Pino A, Hauryliuk V

Mol. Cell 81 (16) 3310-3322.e6 [2021-08-19; online 2021-08-21]

Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data.

Khakzad H, Happonen L, Malmström J, Malmström L

Bioinformatics - (-) - [2021-06-15; online 2021-06-15]

Binding of the human antioxidation protein α1-microglobulin (A1M) to heparin and heparan sulfate. Mapping of binding site, molecular and functional characterization, and co-localization in vivo and in vitro.

Bergwik J, Kristiansson A, Larsson J, ..., Åkerström B, Allhorn M

Redox Biol 41 (-) 101892 [2021-05-00; online 2021-02-10]

The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms.

Hasan M, Khakzad H, Happonen L, ..., Malmström A, Tykesson E

Chem. Sci. 12 (5) 1869-1885 [2021-02-07; online 2020-12-08]

In vivo Cross-Linking MS of the Complement System MAC Assembled on Live Gram-Positive Bacteria.

Khakzad H, Happonen L, Tran Van Nhieu G, Malmström J, Malmström L

Front Genet 11 (-) 612475 [2021-01-08; online 2021-01-08]

Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology.

Khakzad H, Happonen L, Karami Y, ..., Malmström J, Malmström L

PLoS Comput. Biol. 17 (1) e1008169 [2021-01-00; online 2021-01-07]

Year 2020

Structure dynamics of ApoA-I amyloidogenic variants in small HDL increase their ability to mediate cholesterol efflux.

Nilsson O, Lindvall M, Obici L, ..., Lagerstedt JO, Del Giudice R

J. Lipid Res. 62 (-) 100004 [2020-11-24; online 2020-11-24]

A dual-action peptide-containing hydrogel targets wound infection and inflammation.

Puthia M, Butrym M, Petrlova J, ..., Kjellström S, Schmidtchen A

Sci Transl Med 12 (524) eaax6601 [2020-01-01; online 2020-01-03]

Year 2019

The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes.

Betancourt LH, Szasz AM, Kuras M, ..., Sanchez A, Marko-Varga G

Cancers (Basel) 11 (12) - [2019-12-09; online 2019-12-09]

Identification of two abundant Aerococcus urinae cell wall-anchored proteins.

Senneby E, Sunnerhagen T, Hallström B, ..., Karlsson C, Rasmussen M

Int. J. Med. Microbiol. 309 (7) 151325 [2019-11-00; online 2019-06-24]

Novel functional proteins coded by the human genome discovered in metastases of melanoma patients.

Sanchez A, Kuras M, Murillo JR, ..., Betancourt LH, Marko-Varga G

Cell Biol. Toxicol. - (-) - [2019-10-10; online 2019-10-10]

Cold Atmospheric Plasma Disarms M1 Protein, an Important Streptococcal Virulence Factor.

Persson ST, Ekström S, Papareddy P, Herwald H

J Innate Immun 12 (4) 277-290 [2019-09-27; online 2019-09-27]

Global extracellular vesicle proteomic signature defines U87-MG glioma cell hypoxic status with potential implications for non-invasive diagnostics.

Indira Chandran V, Welinder C, Gonçalves de Oliveira K, ..., Marko-Varga G, Belting M

J. Neurooncol. 144 (3) 477-488 [2019-09-00; online 2019-08-14]

Matrisome Properties of Scaffolds Direct Fibroblasts in Idiopathic Pulmonary Fibrosis.

Elowsson Rendin L, Löfdahl A, Åhrman E, ..., Malmström J, Westergren-Thorsson G

Int J Mol Sci 20 (16) - [2019-08-17; online 2019-08-17]

Clinical protein science in translational medicine targeting malignant melanoma.

Gil J, Betancourt LH, Pla I, ..., Malm J, Marko-Varga G

Cell Biol. Toxicol. 35 (4) 293-332 [2019-08-00; online 2019-03-21]

Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma.

Mohlin S, Hansson K, Radke K, ..., von Stedingk K, Bexell D

EMBO Mol Med 11 (8) e10058 [2019-08-00; online 2019-07-16]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service] Structural Proteomics [Service]

Streptococcus pyogenes evades adaptive immunity through specific IgG glycan hydrolysis.

Naegeli A, Bratanis E, Karlsson C, ..., Malmström J, Collin M

J. Exp. Med. 216 (7) 1615-1629 [2019-07-01; online 2019-05-15]

A quantitative Streptococcus pyogenes-human protein-protein interaction map reveals localization of opsonizing antibodies.

Happonen L, Hauri S, Svensson Birkedal G, ..., Malmström L, Malmström J

Nat Commun 10 (1) 2727 [2019-06-21; online 2019-06-21]

Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx.

Awad W, Al-Eryani Y, Ekström S, Logan DT, von Wachenfeldt C

Structure 27 (6) 923-936.e6 [2019-06-04; online 2019-04-11]

Ultrasensitive Immunoprofiling of Plasma Extracellular Vesicles Identifies Syndecan-1 as a Potential Tool for Minimally Invasive Diagnosis of Glioma.

Indira Chandran V, Welinder C, Månsson AS, ..., Sundgren PC, Belting M

Clin. Cancer Res. 25 (10) 3115-3127 [2019-05-15; online 2019-01-24]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development] Structural Proteomics [Service]

Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells.

Mehmeti M, Bergenfelz C, Källberg E, ..., André I, Leandersson K

Commun Biol 2 (1) 176 [2019-05-09; online 2019-05-09]

Greedy de novo motif discovery to construct motif repositories for bacterial proteomes.

Khakzad H, Malmström J, Malmström L

BMC Bioinformatics 20 (Suppl 4) 141 [2019-04-18; online 2019-04-18]

Neutrophil extracellular traps in the central nervous system hinder bacterial clearance during pneumococcal meningitis.

Mohanty T, Fisher J, Bakochi A, ..., Bentzer P, Linder A

Nat Commun 10 (1) 1667 [2019-04-10; online 2019-04-10]

Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data.

Betancourt LH, Pawłowski K, Eriksson J, ..., Jönsson G, Marko-Varga G

Sci Rep 9 (1) 5154 [2019-03-26; online 2019-03-26]

Complement Activation Occurs at the Surface of Platelets Activated by Streptococcal M1 Protein and This Results in Phagocytosis of Platelets.

Palm F, Sjöholm K, Malmström J, Shannon O

J. Immunol. 202 (2) 503-513 [2019-01-15; online 2018-12-12]

Rapid determination of quaternary protein structures in complex biological samples.

Hauri S, Khakzad H, Happonen L, ..., Malmström J, Malmström L

Nat Commun 10 (1) 192 [2019-01-14; online 2019-01-14]

Year 2018

High-efficient bacterial production of human ApoA-I amyloidogenic variants.

Del Giudice R, Lagerstedt JO

Protein Sci. 27 (12) 2101-2109 [2018-12-00; online 2018-10-07]

The Human Salivary Antimicrobial Peptide Profile according to the Oral Microbiota in Health, Periodontitis and Smoking.

Grant M, Kilsgård O, Åkerman S, ..., Malmström J, Jönsson D

J Innate Immun 11 (5) 432-444 [2018-11-28; online 2018-11-28]

Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis.

Åhrman E, Hallgren O, Malmström L, ..., Westergren-Thorsson G, Malmström J

J Proteomics 189 (-) 23-33 [2018-10-30; online 2018-03-01]

Disruption of a GATA1-binding motif upstream of XG/PBDX abolishes Xga expression and resolves the Xg blood group system.

Möller M, Lee YQ, Vidovic K, ..., Storry JR, Olsson ML

Blood 132 (3) 334-338 [2018-07-19; online 2018-05-10]

Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides.

Saravanan R, Holdbrook DA, Petrlova J, ..., Malmsten M, Schmidtchen A

Nat Commun 9 (1) 2762 [2018-07-17; online 2018-07-17]

Streptococcus pyogenes Infection and the Human Proteome with a Special Focus on the Immunoglobulin G-cleaving Enzyme IdeS.

Karlsson CAQ, Järnum S, Winstedt L, ..., Linder A, Malmström JA

Mol. Cell Proteomics 17 (6) 1097-1111 [2018-06-00; online 2018-03-06]

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells.

Guzzi N, Cieśla M, Ngoc PCT, ..., Hsieh AC, Bellodi C

Cell 173 (5) 1204-1216.e26 [2018-05-17; online 2018-04-05]

BAP1 induces cell death via interaction with 14-3-3 in neuroblastoma.

Sime W, Niu Q, Abassi Y, ..., Fu H, Massoumi R

Cell Death Dis 9 (5) 458 [2018-05-01; online 2018-05-01]

Allele-selective RUNX1 binding regulates P1 blood group status by transcriptional control of A4GALT.

Westman JS, Stenfelt L, Vidovic K, ..., Kjellström S, Olsson ML

Blood 131 (14) 1611-1616 [2018-04-05; online 2018-02-08]

Molecularly imprinted polymers synthesized via template immobilization on fumed silica nanoparticles for the enrichment of phosphopeptides.

Duarte M, Subedi P, Yilmaz E, ..., Laurell T, Ekström S

J. Mol. Recognit. 31 (3) - [2018-03-00; online 2017-10-12]

Structural and Biophysical Characterization of Human EXTL3: Domain Organization, Glycosylation, and Solution Structure.

Awad W, Kjellström S, Svensson Birkedal G, Mani K, Logan DT

Biochemistry 57 (7) 1166-1177 [2018-02-20; online 2018-02-05]

Proteomic analyses identify prognostic biomarkers for pancreatic ductal adenocarcinoma.

Hu D, Ansari D, Pawłowski K, ..., Marko-Varga G, Andersson R

Oncotarget 9 (11) 9789-9807 [2018-02-09; online 2018-01-03]

A novel monoclonal antibody targeting carboxymethyllysine, an advanced glycation end product in atherosclerosis and pancreatic cancer.

Wendel U, Persson N, Risinger C, ..., Jansson B, Blixt O

PLoS ONE 13 (2) e0191872 [2018-02-08; online 2018-02-08]

Comprehensive Mass Spectrometric Survey of Streptococcus pyogenes Subcellular Proteomes.

Wilk L, Happonen L, Malmström J, Herwald H

J. Proteome Res. 17 (1) 600-617 [2018-01-05; online 2017-12-04]

Leucocyte recruitment and molecular fortification of keratinocytes triggered by streptococcal M1 protein.

Persson ST, Hauri S, Malmström J, Herwald H

Cell. Microbiol. 20 (1) - [2018-01-00; online 2017-10-19]

Year 2017

MALDIViz: A Comprehensive Informatics Tool for MALDI-MS Data Visualization and Analysis.

Jagadeesan KK, Ekström S

SLAS DISCOVERY: Advancing Life Sciences R&D 22 (10) 1246-1252 [2017-12-00; online 2017-08-21]

Filter Plate-Based Screening of MIP SPE Materials for Capture of the Biomarker Pro-Gastrin-Releasing Peptide.

Jagadeesan KK, Rossetti C, Abdel Qader A, ..., Laurell T, Ekström S

SLAS DISCOVERY: Advancing Life Sciences R&D 22 (10) 1253-1261 [2017-12-00; online 2017-01-31]

Solid-phase extraction of the alcohol abuse biomarker phosphatidylethanol using newly synthesized polymeric sorbent materials containing quaternary heterocyclic groups.

Duarte M, Jagadeesan KK, Billing J, ..., Laurell T, Ekström S

Journal of Chromatography A 1519 (-) 1-8 [2017-10-13; online 2017-08-25]

Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo.

Saravanan R, Adav SS, Choong YK, ..., Sze SK, Schmidtchen A

Sci Rep 7 (1) 13136 [2017-10-13; online 2017-10-13]

Cu/Zn Superoxide Dismutase Forms Amyloid Fibrils under Near-Physiological Quiescent Conditions: The Roles of Disulfide Bonds and Effects of Denaturant.

Khan MAI, Respondek M, Kjellström S, ..., Linse S, Akke M

ACS Chem Neurosci 8 (9) 2019-2026 [2017-09-20; online 2017-06-20]

The TLR2 Antagonist Staphylococcal Superantigen-Like Protein 3 Acts as a Virulence Factor to Promote Bacterial Pathogenicity in vivo.

Koymans KJ, Goldmann O, Karlsson CAQ, ..., van Strijp JAG, Medina E

J Innate Immun 9 (6) 561-573 [2017-09-01; online 2017-09-01]

Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry.

Rolandsson Enes S, Åhrman E, Palani A, ..., Malmström J, Westergren-Thorsson G

Sci Rep 7 (1) 9316 [2017-08-24; online 2017-08-24]

Identification of bacterial biofilm and the Staphylococcus aureus derived protease, staphopain, on the skin surface of patients with atopic dermatitis.

Sonesson A, Przybyszewska K, Eriksson S, ..., Potempa J, Schmidtchen A

Sci Rep 7 (1) 8689 [2017-08-18; online 2017-08-18]

Epitope mapping of a new anti-Tn antibody detecting gastric cancer cells.

Persson N, Stuhr-Hansen N, Risinger C, ..., Jansson B, Blixt O

Glycobiology 27 (7) 635-645 [2017-07-01; online 2017-04-19]

Three-dimensional structures and functional studies of two GH43 arabinofuranosidases from Weissella sp. strain 142 and Lactobacillus brevis.

Linares-Pastén JA, Falck P, Albasri K, ..., Logan DT, Karlsson EN

FEBS J. 284 (13) 2019-2036 [2017-07-00; online 2017-06-18]

Correlation of histopathologic characteristics to protein expression and function in malignant melanoma.

Welinder C, Pawłowski K, Szasz AM, ..., Wieslander E, Marko-Varga G

PLoS ONE 12 (4) e0176167 [2017-04-26; online 2017-04-26]

Year 2016

A Combinatory Antibody-Antigen Microarray Assay for High-Content Screening of Single-Chain Fragment Variable Clones from Recombinant Libraries.

Persson N, Jansson B, Stuhr-Hansen N, ..., Danielsson L, Blixt O

PLoS ONE 11 (12) e0168761 [2016-12-21; online 2016-12-21]

Catalytic Formation of Disulfide Bonds in Peptides by Molecularly Imprinted Microgels at Oil/Water Interfaces.

Shen X, Huang C, Shinde S, ..., Fritz E, Sellergren B

ACS Appl Mater Interfaces 8 (44) 30484-30491 [2016-11-09; online 2016-10-26]

Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry.

Al-Eryani Y, Ib Rasmussen M, Kjellström S, ..., Emanuelsson C, von Wachenfeldt C

Proteins 84 (9) 1234-1245 [2016-09-00; online 2016-06-15]

Metastasis Stimulation by Hypoxia and Acidosis-Induced Extracellular Lipid Uptake Is Mediated by Proteoglycan-Dependent Endocytosis.

Menard JA, Christianson HC, Kucharzewska P, ..., Johansson MC, Belting M

Cancer Res. 76 (16) 4828-4840 [2016-08-15; online 2016-05-19]

Intra-tumour IgA1 is common in cancer and is correlated with poor prognosis in bladder cancer.

Welinder C, Jirström K, Lehn S, ..., Danielsson L, Jansson B

Heliyon 2 (8) e00143 [2016-08-00; online 2016-08-16]

The Aquaporin Splice Variant NbXIP1;1α Is Permeable to Boric Acid and Is Phosphorylated in the N-terminal Domain.

Ampah-Korsah H, Anderberg HI, Engfors A, ..., Kjellbom P, Johanson U

Front Plant Sci 7 (-) 862 [2016-06-16; online 2016-06-16]

Pseudomonas aeruginosa elastase cleaves a C-terminal peptide from human thrombin that inhibits host inflammatory responses.

van der Plas MJ, Bhongir RK, Kjellström S, ..., Mörgelin M, Schmidtchen A

Nat Commun 7 (-) 11567 [2016-05-16; online 2016-05-16]

Multiplexed MALDI-MS arrays for screening of MIP solid phase extraction materials.

Jagadeesan KK, Wierzbicka C, Laurell T, ..., Shinde S, Ekström S

Journal of Chromatography B 1021 (-) 213-220 [2016-05-15; online 2015-10-30]

Hypoxia regulates global membrane protein endocytosis through caveolin-1 in cancer cells.

Bourseau-Guilmain E, Menard JA, Lindqvist E, ..., Welinder C, Belting M

Nat Commun 7 (-) 11371 [2016-04-20; online 2016-04-20]

Elucidating the Molecular Composition of Cartilage by Proteomics.

Hsueh MF, Khabut A, Kjellström S, Önnerfjord P, Kraus VB

J. Proteome Res. 15 (2) 374-388 [2016-02-05; online 2016-01-15]