Per Juris Kraulis

Per Juris Kraulis
Stockholm University | SU · Department of Biochemistry and Biophysics

Ph.D.

About

32
Publications
3,216
Reads
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18,536
Citations
Introduction
Per Kraulis currently works at the Department of Biochemistry and Biophysics , Stockholm University. Per does research in Computing in Mathematics, Natural Science, Engineering and Medicine, Bioinformatics and Biotechnology. He is a Data Engineer with the Data Centre at SciLifeLab.
Additional affiliations
February 2010 - present
Stockholm University
Position
  • Senior Researcher
Description
  • IT Systems Architect, National Genomics Infrastructure
August 2009 - February 2010
Karolinska Institutet
Position
  • Head of Research Informatics

Publications

Publications (32)
Article
Structural and biochemical analysis of proteins requires access to purified protein material. Modern molecular biology technologies facilitate straightforward molecular cloning and expression analysis of multiple protein constructs in parallel, and such approaches have proven very efficient to identify samples suitable for further analysis. A varie...
Article
Computer graphics can be used for the prediction of substrate specificity and stereoselectivity in the α-chymotrypsin catalyzed hydrolysis of Disubstituted propanedioic acid diesters. This enzyme catalyzed reaction is useful for the preparation of chiral starting materials, e.g. for the synthesis of optically pure α-methylaminoacids.
Data
E. coli isozymes Flat file containing a simple list of the isozymes in E. coli.
Data
S. cerevisiae isozymes Flat file containing a simple list of the isozymes in S. cerevisiae.
Article
Full-text available
Background Many biological networks show some characteristics of scale-free networks. Scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. In networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger no...
Article
Full-text available
The two most common models for the evolution of metabolism are the patchwork evolution model, where enzymes are thought to diverge from broad to narrow substrate specificity, and the retrograde evolution model, according to which enzymes evolve in response to substrate depletion. Analysis of the distribution of homologous enzyme pairs in the metabo...
Article
Full-text available
We have determined the solution structure of an albumin binding domain of protein G, a surface protein of group C and G streptococci. We find that it folds into a left handed three-helix bundle similar to the albumin binding domain of protein PAB from Peptostreptococcus magnus. The two domains share 59% sequence identity, are thermally very stable,...
Article
Assignment of NMR spectra is a prerequisite for structure determination of proteins using NMR. The time spent on the assignment is comparatively long compared to that spent on other parts in the protein structure determination process, but it can be shortened by using either interactive or fully automated computer programs. To benefit from the adva...
Chapter
Macromolecular programs and program systems in wide use are described. The chapter covers PHASES; DM/DMMULTI, software for phase improvement by density modification; the structure-determination language of the Crystallography & NMR System; the TNT refinement package; the ARP/wARP suite for automated construction and refinement of protein models; va...
Article
Streptococcal protein G (SPG) is a cell surface receptor protein with a multiple domain structure containing tandem repeats of serum albumin-binding domains (ABD) and immunoglobulin-binding domains (IgBD). In this paper, we have analysed the fold of ABD. Far-UV circular dichroism analysis of ABD indicates high helical content (56%). Based on an ana...
Article
The sequence-specific assignment of resonances is considered to be a requirement for the determination of the three-dimensional (3D) structure of a protein in solution by nuclear magnetic resonance methods. The main source of structural information is the nuclear Overhauser effect spectroscopy (NOESY) spectrum, which contains information about spat...
Article
The sequence-specific assignment of resonances is considered to be a requirement for the determination of the three-dimensional (3D) structure of a protein in solution by nuclear magnetic resonance methods. The main source of structural information is the nuclear Overhauser effect spectroscopy (NOESY) spectrum, which contains information about spat...
Article
A high-resolution solution structure of the GDP form of a truncated version of the ras p21 protein (residues 1-166) has been determined using NMR spectroscopy. Ras p21 is the product of the human ras protooncogene and a member of a ubiquitous eukaryotic gene family which is highly conserved in evolution. A virtually complete assignment (13C, 15N, a...
Article
Full-text available
The conserved, abundant chromosomal protein HMG1 consists of two highly homologous, folded, basic DNA-binding domains, each of approximately 80 amino acid residues, and an acidic C-terminal tail. Each folded domain represents an 'HMG box', a sequence motif recently recognized in certain sequence-specific DNA-binding proteins and which also occurs i...
Article
The function of the cellulose-binding domain (CBD) of the cellobiohydrolase I of Trichoderma reesei was studied by site-directed mutagenesis of two amino acid residues identified by analyzing the 3D structure of this domain. The mutant enzymes were produced in yeast and tested for binding and activity on crystalline cellulose. Mutagenesis of the ty...
Article
Full-text available
The yeast transcriptional activator GAL4 binds co-operatively to four related 17-base-pair sequences within an upstream activating sequence (UASG) to activate transcription of the GAL1 and GAL10 genes. It belongs to a class of gene regulatory proteins which all contain a highly conserved cysteine-rich region within their DNA-binding domains. This r...
Article
Full-text available
The MOLSCRIPT program produces plots of protein structures using several different kinds of representations. Schematic drawings, simple wire models, ball-and-stick models, CPK models and text labels can be mixed freely. The schematic drawings are shaded to improve the illusion of three dimensionality. A number of parameters affecting various aspect...
Chapter
It has long been clear that it should be possible to computerize the assignment of protein 2D NMR spectra to a large degree. Work in this area has mainly focused on various automatic procedures1–7.
Article
The solution structure of a synthetic 36-residue polypeptide comprising the C-terminal cellulose binding domain of cellobiohydrolase I (CT-CBH I) from Trichoderma reesei was investigated by nuclear magnetic resonance (NMR) spectroscopy. The 1H NMR spectrum was completely assigned in a sequential manner by two-dimensional NMR techniques. A large num...
Article
The solution conformation of the antibacterial polypeptide cecropin A from the Cecropia moth is investigated by nuclear magnetic resonance (NMR) spectroscopy under conditions where it adopts a fully ordered structure, as judged by previous circular dichroism studies [Steiner, H. (1982) FEBS Lett. 137, 283-287], namely, 15% (v/v) hexafluoroisopropyl...
Article
Full-text available
The geometric information used to solve three-dimensional (3D) structures of proteins by NMR spectroscopy resides in short (less than 5 A) interproton-distance data. To obtain these distances, the 1H-NMR spectrum must first be assigned using correlation and nuclear Overhauser effect (NOE) experiments to demonstrate through-bond (scalar) and through...
Article
A method to build a three-dimensional protein model from nuclear magnetic resonance (NMR) data using fragments from a data base of crystallographically determined protein structures is presented. The interproton distances derived from the nuclear Overhauser effect (NOE) data are compared to the precalculated distances in the known protein structure...
Chapter
Two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy is a powerful method for studying the three-dimensional structure of small and medium-sized proteins (MW < 10 kD) in solution (Wüthrich et al 1982). Proteins studied by this method include micelle-bound glucagon (Braun et al 1983), lac repressor headpiece (Kaptein et al 1985, Zuiderwe...
Article
Full-text available
Since its first isolation, bovine beta-lactoglobulin (BLG) has been an enigma: although it is abundant in the whey fraction of milk, its function is still not clear. The results of the many physicochemical studies on the protein need a structural interpretation. We report here the structure of the orthorhombic crystal form of cow BLG at pH 7.6, at...
Article
Int. Symp. Trichoderma cellulases, Tricell -89. Vienna, 14 - 16 Sept. 1989. Abstract, 9
Article
Trichoderma reesei Cellulases: Biochemistry, Genetics, Physiology and Application. Ed. by C. P. Kubicek, D. E. Eveleigh, H. Esterbauer, W. Steiner & E. M. Kubicek-Pranz, 156 - 167
Article
2nd Nordic Conference on Protein Engineering.Helsingör, 10 - 11 Oct. 1990, 37
Article
Full-text available
6th Int. Symposium on Genetics of Industrial Microorganisms. Strasbourg, 12 - 18 Aug. 1990, 60

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