Automated building and validation of crystallographic structures of proteins and ligands
12:00pm - 1:00pm /
Friday 18th March 2016
/ Venue: Seminar Room 6, 2nd Floor Life Sciences Building
- Louise Crompton
- Admission: Free
- Book now
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Dr. Victor Lamzin, a senior scientist at EMBL Hamburg since 2003, will be visiting IIB's Dr Antonyuk and Prof Hasnain during 17-19 March 2016. Lamzin’s research group applies and develops cutting-edge computational and experimental approaches for structural biology, with a major focus in macromolecular crystallography.
Lamzin’s group development - (ARP/wARP - one of the leading software for macromolecular structure determination with an excellent record of solved structures, performance and functionality. His landmark paper on ARP/wARP [Perrakis, Morris, Lamzin. Automated protein model building combined with iterative structure refinement. Nature Struct Biol 1999; 6:458-463] has gathered almost 3,000 citations and is the most cited paper published in this journal.
The knowledge of the structures of biological macromolecules is imperative for the understanding of their function in cellular processes and their role in human diseases. The rapidly growing Protein Data Bank now contains 115,000 three-dimensional structures of proteins and nucleic acids. Deciphering and validating these structures is essential for biological research.
The description of protein polypeptide chain is typically done using the Ramachandran plot, which provides simple conformational depiction of each residue in the model. However, an increasingly often observed natural variation of the polypeptide stereochemistry calls for the use of more elaborate tools. Within the ARP/wARP software project for macromolecular crystallographic model building and refinement, we have developed a novel distance-geometry-based approach, presenting protein stereochemistry in a Euclidian orthogonal three-dimensional space. The application of the method to model building and validation will be discussed.
In addition to building protein structures, we develop methods for modelling of bound ligands. This faces several challenges: the vast universe of small molecules of different shapes and topologies; partial disorder of bound ligands; and multiple overlapping ligand networks. The current state of ligand building with ARP/wARP will be presented, alongside a novel validation method, which evaluates the interactions of the ligand with the protein.
References
Giewekemeyer K, Hackenberg C, Aquila A, Wilke RN, Groves MR, Jordanova R, Lamzin VS, Borchers G, Saksl K, Zozulya AV, Sprung M, Mancuso AP. (2015) Tomography of a cryo-immobilized yeast cell using ptychographic coherent X-ray Diffractive imaging. Biophys J. 109, 1986-1995. PMID: 26536275
Carolan CG, Lamzin VS. Automated identification of crystallographic ligands using sparse-density representations. (2014) Acta Crystallogr D Biol Crystallogr. 70, 1844-1853. PMID: 25004962
Hattne J, Lamzin VS. (2011) A moment invariant for evaluating the chirality of three-dimensional objects. J R Soc Interface. 8, 144-151. PMID: 20685692
Langer G, Cohen SX, Lamzin VS, Perrakis A. (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc. 3, 1171-1179. PMID: 18600222
Lamzin’s group development - (ARP/wARP - one of the leading software for macromolecular structure determination with an excellent record of solved structures, performance and functionality. His landmark paper on ARP/wARP [Perrakis, Morris, Lamzin. Automated protein model building combined with iterative structure refinement. Nature Struct Biol 1999; 6:458-463] has gathered almost 3,000 citations and is the most cited paper published in this journal.
The knowledge of the structures of biological macromolecules is imperative for the understanding of their function in cellular processes and their role in human diseases. The rapidly growing Protein Data Bank now contains 115,000 three-dimensional structures of proteins and nucleic acids. Deciphering and validating these structures is essential for biological research.
The description of protein polypeptide chain is typically done using the Ramachandran plot, which provides simple conformational depiction of each residue in the model. However, an increasingly often observed natural variation of the polypeptide stereochemistry calls for the use of more elaborate tools. Within the ARP/wARP software project for macromolecular crystallographic model building and refinement, we have developed a novel distance-geometry-based approach, presenting protein stereochemistry in a Euclidian orthogonal three-dimensional space. The application of the method to model building and validation will be discussed.
In addition to building protein structures, we develop methods for modelling of bound ligands. This faces several challenges: the vast universe of small molecules of different shapes and topologies; partial disorder of bound ligands; and multiple overlapping ligand networks. The current state of ligand building with ARP/wARP will be presented, alongside a novel validation method, which evaluates the interactions of the ligand with the protein.
References
Giewekemeyer K, Hackenberg C, Aquila A, Wilke RN, Groves MR, Jordanova R, Lamzin VS, Borchers G, Saksl K, Zozulya AV, Sprung M, Mancuso AP. (2015) Tomography of a cryo-immobilized yeast cell using ptychographic coherent X-ray Diffractive imaging. Biophys J. 109, 1986-1995. PMID: 26536275
Carolan CG, Lamzin VS. Automated identification of crystallographic ligands using sparse-density representations. (2014) Acta Crystallogr D Biol Crystallogr. 70, 1844-1853. PMID: 25004962
Hattne J, Lamzin VS. (2011) A moment invariant for evaluating the chirality of three-dimensional objects. J R Soc Interface. 8, 144-151. PMID: 20685692
Langer G, Cohen SX, Lamzin VS, Perrakis A. (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc. 3, 1171-1179. PMID: 18600222