Bernhard Lohkamp

About me
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About me

Teacher and structural biologist...

Research

My research focuses on the development of methods for (graphical) model building and map interpretation used in structural biology (Coot). More information about WinCoot: http://bernhardcl.github.io/coot/ Furthermore, I am interested in protein-protein complexes involved in nerve cell development, esp. the axon, as well as its implication in disease and nerve cell repair. Various complexes constituting a variety of proteins (e.g. enzymes, motor proteins) are investigated functionally and structurally.

Teaching

Teaching chemistry and structure biology related subjects. Course director in Biomedicine Bachelor (General and Organic Chemistry, Chemical Biology) and Master (Frontiers in Biomedicine: Research Project 1) programme. Teaching crystallography in workshops worldwide.

Articles

Journal article: BIOMOLECULES. 2023;13(12):1763

The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces.

Cederfelt D; Badgujar D; Au Musse A; Lohkamp B; Danielson UH; Dobritzsch D
Journal article: ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY. 2023;79(Pt 6):449-461

The CCP4 suite: integrative software for macromolecular crystallography.

Agirre J; Atanasova M; Bagdonas H; Ballard CB; Baslé A; Beilsten-Edmands J; Borges RJ; Brown DG; Burgos-Mármol JJ; Berrisford JM; Bond PS; Caballero I; Catapano L; Chojnowski G; Cook AG; Cowtan KD; Croll TI; Debreczeni JÉ; Devenish NE; Dodson EJ; Drevon TR; Emsley P; Evans G; Evans PR; Fando M; Foadi J; Fuentes-Montero L; Garman EF; Gerstel M; Gildea RJ; Hatti K; Hekkelman ML; Heuser P; Hoh SW; Hough MA; Jenkins HT; Jiménez E; Joosten RP; Keegan RM; Keep N; Krissinel EB; Kolenko P; Kovalevskiy O; Lamzin VS; Lawson DM; Lebedev AA; Leslie AGW; Lohkamp B; Long F; Malý M; McCoy AJ; McNicholas SJ; Medina A; Millán C; Murray JW; Murshudov GN; Nicholls RA; Noble MEM; Oeffner R; Pannu NS; Parkhurst JM; Pearce N; Pereira J; Perrakis A; Powell HR; Read RJ; Rigden DJ; Rochira W; Sammito M; Sánchez Rodríguez F; Sheldrick GM; Shelley KL; Simkovic F; Simpkin AJ; Skubak P; Sobolev E; Steiner RA; Stevenson K; Tews I; Thomas JMH; Thorn A; Valls JT; Uski V; Usón I; Vagin A; Velankar S; Vollmar M; Walden H; Waterman D; Wilson KS; Winn MD; Winter G; Wojdyr M; Yamashita K
Article: ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY. 2022;78(Pt 9):1079-1089

CCP4 Cloud for structure determination and project management in macromolecular crystallography.

Krissinel E; Lebedev AA; Uski V; Ballard CB; Keegan RM; Kovalevskiy O; Nicholls RA; Pannu NS; Skubák P; Berrisford J; Fando M; Lohkamp B; Wojdyr M; Simpkin AJ; Thomas JMH; Oliver C; Vonrhein C; Chojnowski G; Basle A; Purkiss A; Isupov MN; McNicholas S; Lowe E; Triviño J; Cowtan K; Agirre J; Rigden DJ; Uson I; Lamzin V; Tews I; Bricogne G; Leslie AGW; Brown DG
Article: AMERICAN JOURNAL OF HUMAN GENETICS. 2021;108(5):951-961

Missense variants in DPYSL5 cause a neurodevelopmental disorder with corpus callosum agenesis and cerebellar abnormalities.

Jeanne M; Demory H; Moutal A; Vuillaume M-L; Blesson S; Thépault R-A; Marouillat S; Halewa J; Maas SM; Motazacker MM; Mancini GMS; van Slegtenhorst MA; Andreou A; Cox H; Vogt J; Laufman J; Kostandyan N; Babikyan D; Hancarova M; Bendova S; Sedlacek Z; Aldinger KA; Sherr EH; Argilli E; England EM; Audebert-Bellanger S; Bonneau D; Colin E; Denommé-Pichon A-S; Gilbert-Dussardier B; Isidor B; Küry S; Odent S; Redon R; Khanna R; Dobyns WB; Bézieau S; Honnorat J; Lohkamp B; Toutain A; Laumonnier F
Article: PROTEIN SCIENCE. 2020;29(4):1069-1078

Current developments in Coot for macromolecular model building of Electron Cryo-microscopy and Crystallographic Data.

Casañal A; Lohkamp B; Emsley P
Article: BIOCHEMICAL JOURNAL. 2018;475(14):2395-2416

Crystal structure and pH-dependent allosteric regulation of human β-ureidopropionase, an enzyme involved in anticancer drug metabolism.

Maurer D; Lohkamp B; Krumpel M; Widersten M; Dobritzsch D
Article: JOURNAL OF PHYSICAL CHEMISTRY LETTERS. 2018;9(14):4082-4086

Mass Spectrometry Reveals the Direct Action of a Chemical Chaperone.

Gault J; Lianoudaki D; Kaldmäe M; Kronqvist N; Rising A; Johansson J; Lohkamp B; Laín S; Allison TM; Lane DP; Marklund EG; Landreh M
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2017;114(14):3637-3641

Ab initio solution of macromolecular crystal structures without direct methods.

McCoy AJ; Oeffner RD; Wrobel AG; Ojala JRM; Tryggvason K; Lohkamp B; Read RJ
Article: PLOS ONE. 2015;10(3):e0121494

Crystal structures of the kinase domain of the sulfate-activating complex in Mycobacterium tuberculosis.

Poyraz Ö; Brunner K; Lohkamp B; Axelsson H; Hammarström LGJ; Schnell R; Schneider G
Article: ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY. 2014;70(Pt 6):1680-1694

Crystal structure of human CRMP-4: correction of intensities for lattice-translocation disorder.

Ponnusamy R; Lebedev AA; Pahlow S; Lohkamp B
Article: JOURNAL OF NEUROCHEMISTRY. 2013;125(6):855-868

Insights into the oligomerization of CRMPs: crystal structure of human collapsin response mediator protein 5.

Ponnusamy R; Lohkamp B
Article: PEDIATRIC NEPHROLOGY. 2013;28(2):339-343

Novel INF2 mutation p. L77P in a family with glomerulopathy and Charcot-Marie-Tooth neuropathy.

Rodriguez PQ; Lohkamp B; Celsi G; Mache CJ; Auer-Grumbach M; Wernerson A; Hamajima N; Tryggvason K; Patrakka J
Journal article: TIJDSCHRIFT VOOR KINDERGENEESKUNDE. 2013;81(Suppl 1):73-74

β-Ureidopropionase deficiency: phenotype, genotype and protein structural consequences in 16 patients

van Kuilenburg ABP; Dobritzsch D; Meijer J; Krumpel M; Selim LA; Rashed MS; Assmann B; Meinsma R; Lohkamp B; Ito T; Abeling NGGM; Saito K; Eto K; Smitka M; Engvall M; Zhang C; Xu W; Zoetekouw L; Hennekam RCM
Article: PLOS ONE. 2013;8(6):e66936

Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates.

Chen MW; Lohkamp B; Schnell R; Lescar J; Schneider G
Article: BIOCHIMICA ET BIOPHYSICA ACTA: INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND BIOPHYSICS. 2012;1822(7):1096-1108

ß-ureidopropionase deficiency: phenotype, genotype and protein structural consequences in 16 patients.

van Kuilenburg ABP; Dobritzsch D; Meijer J; Krumpel M; Selim LA; Rashed MS; Assmann B; Meinsma R; Lohkamp B; Ito T; Abeling NGGM; Saito K; Eto K; Smitka M; Engvall M; Zhang C; Xu W; Zoetekouw L; Hennekam RCM
Article: BIOCHIMICA ET BIOPHYSICA ACTA: INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND BIOPHYSICS. 2010;1804(12):2198-2206

Insights into the mechanism of dihydropyrimidine dehydrogenase from site-directed mutagenesis targeting the active site loop and redox cofactor coordination.

Lohkamp B; Voevodskaya N; Lindqvist Y; Dobritzsch D
Article: ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY. 2010;66(Pt 4):486-501

Features and development of Coot.

Emsley P; Lohkamp B; Scott WG; Cowtan K
Article: JOURNAL OF MOLECULAR BIOLOGY. 2008;377(5):1544-1559

The crystal structure of beta-alanine synthase from Drosophila melanogaster reveals a homooctameric helical turn-like assembly.

Lundgren S; Lohkamp B; Andersen B; Piskur J; Dobritzsch D
Article: ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY. 2008;64(Pt 4):407-415

A mixture of fortunes: the curious determination of the structure of Escherichia coli BL21 Gab protein.

Lohkamp B; Dobritzsch D
Article: MOLECULAR GENETICS AND METABOLISM. 2007;91(2):157-164

Clinical, biochemical and genetic findings in two siblings with a dihydropyrimidinase deficiency.

van Kuilenburg ABP; Meijer J; Dobritzsch D; Meinsma R; Duran M; Lohkamp B; Zoetekouw L; Abeling NGGM; van Tinteren HLG; Bosch AM
Article: JOURNAL OF MOLECULAR BIOLOGY. 2006;362(3):555-566

Three-dimensional structure of iminodisuccinate epimerase defines the fold of the MmgE/PrpD protein family.

Lohkamp B; Bäuerle B; Rieger P-G; Schneider G
Article: JOURNAL OF STRUCTURAL BIOLOGY. 2006;155(1):111-113

Application of a new vector system for efficient protein purification in the crystallization of PA5104/ORF from Pseudomonas aeruginosa.

Lohkamp B; Paterson NG; Lapthorn AJ
Article: JOURNAL OF MOLECULAR BIOLOGY. 2006;359(3):728-740

Crystal structures of SnoaL2 and AclR: two putative hydroxylases in the biosynthesis of aromatic polyketide antibiotics.

Beinker P; Lohkamp B; Peltonen T; Niemi J; Mäntsälä P; Schneider G
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2006;281(19):13762-13776

The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity.

Lohkamp B; Andersen B; Piškur J; Dobritzsch D
Article: ACTA CRYSTALLOGRAPHICA SECTION F: STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS. 2006;62(Pt 1):36-38

Purification, crystallization and X-ray diffraction analysis of dihydropyrimidinase from Dictyostelium discoideum.

Lohkamp B; Andersen B; Piskur J; Dobritzsch D
Article: JOURNAL OF MOLECULAR BIOLOGY. 2004;336(1):131-144

The structure of Escherichia coli ATP-phosphoribosyltransferase: identification of substrate binding sites and mode of AMP inhibition.

Lohkamp B; McDermott G; Campbell SA; Coggins JR; Lapthorn AJ
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2001;276(23):19954-19958

The allosteric effector l-lactate induces a conformational change of 2x6-meric lobster hemocyanin in the oxy state as revealed by small angle x-ray scattering.

Hartmann H; Lohkamp B; Hellmann N; Decker H
Article: ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY. 2000;56(Pt 11):1488-1491

Purification, crystallization and preliminary X-ray crystallographic analysis of ATP-phosphoribosyltransferase from Escherichia coli.

Lohkamp B; Coggins JR; Lapthorn AJ
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All other publications

Corrigendum: PLOS ONE. 2015;10(4):e0127016

Correction: Crystal Structures of the Kinase Domain of the Sulfate-Activating Complex in Mycobacterium tuberculosis.

PLOS ONE Staff
Book chapter: 2012;p. 443-447

Macromolecular model building and validation using Coot

Emsley P; Lohkamp B; Cowtan K
Published paper: NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS. 2008;27(6):809-815

Identification of two novel mutations C79X and R235Q in the dihydropyrimidine dehydrogenase gene in a patient presenting with hematuria.

van Kuilenburg ABP; Meijer J; Dobritzsch D; Lohkamp B; Ruitenbeek W; Roelofsen J; Abeling NGGM; Duran M; Buzing C

Grants

Pushing the limits: Getting more information out of macromolecular structures

Swedish Research Council

1 January 2013 - 31 December 2014
Structural studies on the enzymes of histidine biosynthesis from pathogenic organisms.

Wellcome Trust

1 October 1999 - 30 September 2002

Employments

Senior Lecturer, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 2019-

Degrees and Education

Docent, Karolinska Institutet, 2014

About me

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