Biomedical subjects

Mats Wikström

Publications and source records attributed to Mats Wikström.

9 recordsLinked to original sources

PubMed2004

Crystal structure and biological implications of a bacterial albumin binding module in complex with human serum albumin.

Many bactericide species express surface proteins that interact with human serum albumin (HSA). Protein PAB from the anaerobic bacterium Finegoldia magna (formerly Peptostreptococcus magnus) represents one of these proteins. Protein PAB contains a domain of 53 amino acid residues known as the GA module. GA homologs are also found in protein G of group C and G streptococci. Here we report the crystal structure of HSA in complex with the GA module of protein PAB. The model of the complex was refined to a resolution of 2.7 A and reveals a novel binding epitope located in domain II of the albumin molecule. The GA module is composed of a left-handed three-helix bundle, and residues from the second helix and the loops surrounding it were found to be involved in HSA binding. Furthermore, the presence of HSA-bound fatty acids seems to influence HSA-GA complex formation. F. magna has a much more restricted host specificity compared with C and G streptococci, which is also reflected in the binding of different animal albumins by proteins PAB and G. The structure of the HSA-GA complex offers a molecular explanation to this unusually clear example of bacterial adaptation.

Albumins↗

PubMed2002

Structure-based screening as applied to human FABP4: a highly efficient alternative to HTS for hit generation.

The time-limiting step in HTS often is the development of an appropriate assay. In addition, hits from HTS fairly often turn out to be false positives and generally display unfavorable properties for further development. Here we describe an alternative process for hit generation, applied to the human adipocyte fatty acid binding protein FABP4. A small molecular ligand for FABP4 that blocks the binding of endogenous ligands may be developed into a drug for the treatment of type-2 diabetes. Using NMR spectroscopy, we screened FABP4 for low-affinity binders in a diversity library consisting of small soluble scaffolds, which yielded 52 initial hits in total. The potencies of these hits were ranked, and crystal structures of FABP4 complexes for two of the hits were obtained. The structural data were subsequently used to direct similarity searches for available analogues, as well as chemical synthesis of 12 novel analogues. In this way, a series of three selective FABP4 ligands with attractive pharmacochemical profiles and potencies of 10 microM or better was obtained.

Amino Acid Sequence↗

PubMed2002

Identification of two protein-binding and functional regions of curli, a surface organelle and virulence determinant of Escherichia coli.

Curli are surface organelles of Escherichia coli. These fibrous proteins, formed by polymerization of a 15-kDa subunit, are expressed by E. coli strains associated with severe infections in humans. A remarkable property of curli is their ability to interact with a wide range of human proteins, interactions that contribute to the enhanced virulence of curli-expressing E. coli. To define the protein-binding region(s) of curli, we investigated the binding properties of overlapping synthetic peptides covering the curli subunit. Two peptides, one covering a 24-amino acid residue sequence in the NH(2)-terminal half of the subunit (NNS24) and one corresponding to the 26 COOH-terminal residues (VDQ26), were found to bind a number of human proteins. Physiochemical analysis revealed that NNS24 adopts a thermally stable beta-structure, and in solution the peptide forms soluble multimers, predominantly octamers. Intact curli are known to activate the proinflammatory and procoagulant contact system, and when added to human plasma, the NNS24 and VDQ26 peptides induced the release of the potent vasoactive peptide bradykinin. The results map important curli functions to the regions corresponding to the NNS24 and VDQ26 sequences.

Amino Acid Sequence↗

PubMed2002

Structure-based screening and design in drug discovery.

Structure-based screening represents an integrated approach for the identification and optimization of hits by the combined use of nuclear magnetic resonance (NMR) spectroscopy, homology modeling and X-ray crystallography. A general feature of the methodology is the introduction of structure-based methods (NMR, modeling and X-ray) early in the drug discovery process to optimize hits in terms of their affinities and specificities. This approach promises to deliver leads with improved physicochemical properties as compared with leads generated from a traditional HTS program. This review presents examples of structure-based screening from published and in-house drug discovery projects.

Crystallography, X-Ray↗

PubMed2002

Site-selective screening by NMR spectroscopy with labeled amino acid pairs.

A new method for site-selective screening by NMR is presented. The core of the new method is the dual amino acid sequence specific labeling technique. Amino acid X is labeled with (13)C and amino acid Y is labeled with (15)N. Provided only one XY pair occurs in the amino acid sequence, only one signal in the 1D carbonyl (13)C spectrum will display a splitting due to the (1)J(C'N) coupling. Using this labeling strategy it is possible to screen selectively for binding to a selected epitope without the need for sequence specific assignments. An HNCO spectrum (1D or 2D) can be used either directly as a screening experiment or indirectly to identify what signals to monitor in a 2D (1)H-(15)N correlation spectrum. Chemical shift perturbations upon addition of a potential ligand are easily detected even for large proteins due to the reduced spectral complexity resulting from the use of a selectively labeled sample. The new technique is demonstrated on the human adipocyte fatty acid binding protein FABP-4. Due to the reduced spectral complexity, the method should be applicable to larger proteins than are conventional methods.

Amino Acids↗

PubMed2002

Differences in backbone dynamics of two homologous bacterial albumin-binding modules: implications for binding specificity and bacterial adaptation.

Proteins G and PAB are bacterial albumin-binding proteins expressed at the surface of group C and G streptococci and Peptostreptococcus magnus, respectively. Repeated albumin-binding domains, known as GA modules, are found in both proteins. The third GA module of protein G from the group G streptococcal strain G148 (G148-GA3) and the second GA module of protein PAB from P.magnus strain ALB8 (ALB8-GA) exhibit 59% sequence identity and both fold to form three-helix bundle structures that are very stable against thermal denaturation. ALB8-GA binds human serum albumin with higher affinity than G148-GA3, but G148-GA3 shows substantially broader albumin-binding specificity than ALB8-GA. The (15)N nuclear magnetic resonance spin relaxation measurements reported here, show that the two GA modules exhibit mobility on the picosecond-nanosecond time scale in directly corresponding regions (loops and termini). Most residues in G148-GA3 were seen to be involved in conformational exchange processes on the microsecond-millisecond time scale, whereas for ALB8-GA such motions were only identified for the beginning of helix 2 and its preceding loop. Furthermore, and more importantly, hydrogen-deuterium exchange and saturation transfer experiments reveal large differences between the two GA modules with respect to motions on the second-hour time scale. The high degree of similarity between the two GA modules with respect to sequence, structure and stability, and the observed differences in dynamics, binding affinity and binding specificity to different albumins, suggest a distinct correlation between dynamics, binding affinity and binding specificity. Finally, it is noteworthy in this context that the module G148-GA3, which has broad albumin-binding specificity, is expressed by group C and G streptococci known to infect all mammalian species, whereas P.magnus with the ALB8-GA module has been isolated only from humans.

Adaptation, Physiological↗

PubMed2002

Site-selective labeling strategies for screening by NMR.

NMR based screening has become an important tool in the pharmaceutical industry. Methods that provide information on the location of small molecule binding sites on the surface of a drug target (e. g. SAR-by-NMR and related techniques) are of particular interest. In order to extend the applicability of such techniques to drug targets of higher molecular weight, selective labeling strategies may be employed. Dual-amino acid selective labeling and site directed non-native amino acid replacement (SNAAR) allow for the selective detection of NMR resonances of a specific amino acid residue. This results in significantly reduced spectral complexity, which not only enables application to higher molecular weight systems, but also eliminates the need for sequential resonance assignment in order to identify the binding site. Regio-selective (or segmental) labeling of an entire protein domain of a multi domain protein may also be achieved. Labeling only a selected part of a multi domain protein (e. g. a catalytic or ligand binding domain) is an attractive way to simplify the spectral interpretation without disturbing the system under study.

Amino Acid Sequence↗

PubMed2001

Structure, specificity, and mode of interaction for bacterial albumin-binding modules.

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, and bind to the same site on human serum albumin. The albumin binding site, the first determined for this structural motif known as the GA module, comprises residues spanning the first loop to the beginning of the third helix and includes the most conserved region of GA modules. The two GA modules have different affinities for albumin from different species, and their albumin binding patterns correspond directly to the host specificity of C/G streptococci and P. magnus, respectively. These studies of the evolution, structure, and binding properties of the GA module emphasize the power of bacterial adaptation and underline ecological and medical problems connected with the use of antibiotics.

Amino Acid Sequence↗

PubMedDate not supplied

Percutaneous treatment of hepatocellular carcinoma in patients with transjugular intrahepatic portosystemic shunts.

PURPOSE: To assess the role of transcatheter arterial chemoembolization (TACE) and percutaneous ethanol injection (PEI) in patients with hepatocellular carcinoma (HCC) and transjugular intrahepatic portosystemic shunts (TIPS). METHODS: Between January 1999 and September 2004, 6 patients with HCC and TIPS were treated with either TACE (n = 3) or TACE in combination with PEI (n = 3). One patient had a known advanced, untreated HCC prior to TIPS. In the remaining 5 patients HCC was diagnosed 14, 17, 51, 69, and 76 months respectively after elective TIPS. TACE was performed using a mixture of 30-60 mg of epirubicin and 10 ml of lipiodol following superselective catheterization of tumor-feeding vessels. PEI was performed under CT guidance. METHODS: The mean follow-up time after treatment of HCC was 26.2 months (range 7-46 months). During follow-up, all patients were free of rebleeding. Two patients died 7 and 38 months after one session of TACE and PEI (77 months after TIPS) and three sessions of TACE (91 months after TIPS), respectively. The cause of death was liver failure (Child-Pugh class C) and peritonitis, respectively. A third patient underwent liver transplantation 24 months after TIPS and several sessions of TACE. In the remaining 3 patients, the HCC is well controlled 13, 30, and 46 months after repetitive percutaneous treatment without signs of hepatic deterioration or metastasis. CONCLUSION: Transcatheter arterial superselective chemoembolization and percutaneous ethanol injection seems to be beneficial even in HCC patients treated with TIPS, provided that the liver function is adequate.

Aged↗