structural biology

RESEARCH PORTFOLIO IN
MASS SPECTROMETRY  

PROTEIN PRIMARY STRUCTURES & POST-TRANSLATIONAL MODIFICATIONS

High-resolution mass spectrometry, such as a Fourier transform ion cyclotron resonance (FT-ICR) technique, provides a powerful tool to characterize protein primary structure and its modifications. A determination of the amino acid sequence is one of the primary tasks along a detailed structural characterization of any endogenous or recombinant protein. By simply measuring an intact protein mass with high mass accuracy one can make conclusions with high confidence about the correctness of a given sequence and any possible modifications therein. For instance, small structural changes, such as the formation of a disulfide (-2 Da) or a protein deamidation (+ 1 Da), can be directly detected. In addition, an intrinsic molecular heterogeneity can be detected without preceding chromatographic separation as all different protein forms can be easily resolved. Further identification can be accomplished by enzymatic digestion followed by direct measurement of a resulting peptide mixture or by tandem mass spectrometry of the intact protein ions.

In recent years, we have applied the FT-ICR technique coupled with electrospray ionization (ESI) in the structural characterization of many recombinant and endogenous proteins to verify their sequences and to identify and further locate and quantify post-translational modifications (e.g., deamidations, disulfide formation, heterogeneous glycosylations etc). In these studies, it has been shown that the specificity, sensitivity and accuracy of the technique by far exceed those of classical biophysical and biochemical methods.

Ahmad F, Jänis J, Valjakka J, Isoniemi S, Vainiotalo P, Vullo D, Supuran CT, Waheed A, Sly WS, Niemelä O & Parkkila S: Modification of carbonic anhydrase II with acetaldehyde, the first metabolite of ethanol, leads to decreased enzyme activity. BMC Biochem. (2008) 9:32.

Helppolainen SH, Määttä JA E, Halling KK, Slotte JP, Hytönen VP, Jänis J, Vainiotalo P, Kulomaa MS & Nordlund HR: Bradavidin II from Bradyrhizobium japonicum; A new avidin-like biotin-binding protein. BBA Proteins Proteom. 1784 (2008) 1002-1010.

Määttä JAE, Airanne TT, Nordlund HR, Jänis J, Paldanius TA, Vainiotalo P, Johnson MS, Kulomaa MS & Hytönen VP: Rational modification of ligand-binding preference of avidin by circular permutation and mutagenesis. ChemBioChem 9 (2008) 1124-1135.

Yu L, Zhang B, Szilvay GR, Sun R, Jänis J, Cui Y, Feng S, Xu H, Linder MB & Qiao M: Protein HGFI from the edible mushroom Grifola frondosais a novel 8 kDa class I hydrophobin that forms rodlets in compressed monolayers. Microbiology 154 (2008) 1677-1685.

Helppolainen SH, Nurminen KP, Määttä JAE, Halling KK, Slotte PJ, Huhtala T, Liimatainen T, Ylä-Herttuala S, Airanne KJ, Närvänen A, Jänis J, Vainiotalo P, Valjakka J, Kulomaa MS & Nordlund HR: Rhizavidin from Rhizobium etli – the first natural dimer in the avidin protein family. Biochem. J. 405 (2007) 397-405.

Marjasvaara A, Kruus K & Vainiotalo P: A laccase study by electrospray ionization Fourier transform ion cyclotron resonance MS: copper depletion, glycoforms and stability. J. Mass Spectrom. 41 (2006) 91-97.

Jänis J, Turunen O, Leisola M, Derrick PJ. Rouvinen J & Vainiotalo P: Characterization of mutant xylanases using Fourier transform ion cyclotron resonance mass spectrometry: Stabilizing contributions of disulfide bridges and N-terminal extensions. Biochemistry 43 (2004) 9556-9566.

Xiong H, Jänis J, Leisola M & Turunen O: Characterization of the xylanase produced by submerged cultivation of Thermomyces lanuginosus DSM 10635. Enzyme Microb. Technol. 35 (2004) 93-99.

Fenel F, Leisola M, Jänis J & Turunen O: A de novo designed N-terminal disulphide bridge stabilizes the Trichoderma reesei endo-1,4-b-xylanase II. J. Biotechnol. 108 (2004) 137-143.

Hakulinen N, Turunen O, Jänis J, Leisola M & Rouvinen J: Three-dimensional structures of thermophilic b-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability. Eur. J. Biochem. 270 (2003) 1399-1412.