High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry

Young, Malin M.; Tang, Ning; Hempel, Judith C.; Oshiro, Connie; Taylor, Eric W.; Kuntz, Irwin D.; Gibson, Bradford W.; Dollinger, Gavin

doi:10.1073/pnas.090099097

Cited by 428 publications

(510 citation statements)

References 33 publications

Supporting

Mentioning

503

Contrasting

Unclassified

Order By: Relevance

“…Since acetylated y6 can come from modification of Lys 29 and Tyr 27 and an increase in the y6 ϩ Ac:y6 ratio is not observed, the majority of the modified product must be coming from modification of Lys 29 at pH 8. 4.…”

Section: Methodsmentioning

confidence: 99%

“…However, the promise of intra-molecular crosslinking for structural modeling has only recently been enabled by state of the art mass spectrometric methods that make determination of the cross-linked residues in a protein practical on a reasonable time scale and with small quantities of protein. The first study to derive a sufficient number of intra-molecular distance constraints to develop a structural model for a protein used fibroblast growth factor 2 (FGF-2) as a test case [4]. FGF-2 is a 17 kDa protein, which has 14 lysines evenly dispersed in its 155 residue sequence.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Strategy for selective chemical cross-linking of tyrosine and lysine residues

Leavell

Novák

Behrens

et al. 2004

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

Chemical cross-linking of proteins combined with mass spectral analysis is a powerful technique that can be utilized to yield protein structural information, such as the spatial arrangement of multi-protein complexes or the folding of monomeric proteins. The succinimidyl ester cross-linking reagents are commonly used to cross-link primary amine-containing amino acids (N-terminus and lysine). However, in this study they were used to react with tyrosines as well, which allowed for the formation of cross-links between two primary amines, one primary amine and one tyrosine, or two tyrosines. This result is extremely important to the chemical cross-linking community for two reasons: (1) all possible cross-linked residues must be considered when analyzing data from these experiments to generate correct distance constraints and structural information, and (2) utilizing the versatility of these cross-linking reagents allows more information content to be generated from a single cross-linking reagent, which may increase the number of cross-links obtained in the experiment. Herein, we study the reactivity of the succinimidyl ester labeling and cross-linking reagents with angiotensin I and oxidized insulin ␤-chain. Using the succinimidyl acetate labeling reagent, the reactivity of the N-terminus was found to be greater than either lysine or tyrosine. However, a selectivity of the cross-linking reagent was observed for either tyrosine or lysine depending on the pH of the reaction solution. In acidic pH, it was observed that tyrosine was more reactive, while in alkaline pH lysine was more reactive. Exploiting this selectivity predominantly N-terminustyrosine or tyrosine-tyrosine cross-links were favored at acidic pH, while N-terminus-tyrosine or tyrosine-lysine cross-links were favored at alkaline pH. I nter-molecular chemical cross-linking has a long history as a tool for the study of the quaternary structure of protein complexes [1,2], and many years ago it was suggested that intra-molecular cross-linking could be used as a method of obtaining distance constraints that would be useful in developing structural models of proteins [3]. However, the promise of intra-molecular crosslinking for structural modeling has only recently been enabled by state of the art mass spectrometric methods that make determination of the cross-linked residues in a protein practical on a reasonable time scale and with small quantities of protein. The first study to derive a sufficient number of intra-molecular distance constraints to develop a structural model for a protein used fibroblast growth factor 2 (FGF-2) as a test case [4]. FGF-2 is a 17 kDa protein, which has 14 lysines evenly dispersed in its 155 residue sequence. Using only the commercially available primary amine reactive cross-linker bis(sulfosuccinimidyl) suberate, 18 cross-links were found in FGF-2 in this study, of which 15 provided useful distance constraints for determining the fold family of the protein. Using these 15 constraints it was possible to assign the FGF2 to the corr...

show abstract

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Strategy for selective chemical cross-linking of tyrosine and lysine residues

Leavell

Novák

Behrens

et al. 2004

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

show abstract

“…These peptides were of little value in providing the 3-D spatial constraints, because BS 3 coupling with two lysines could span up to 7 amino acids [14]. The remaining long-span internal crosslinking between K412 and K420 of the Subdomain IIIA, as well as the 9 through-space lysine cross-linking, should provide valuable information on the distance constraints in the 3-D structure of BSA.…”

Section: Distance Constraints Of Lysines In Bsamentioning

confidence: 99%

Probing three-dimensional structure of bovine serum albumin by chemical cross-linking and mass spectrometry

Huang

Kim

Dass

2004

J. Am. Soc. Mass Spectrom.

454

291

View full text Add to dashboard Cite

Serum albumin is the principal transporter of fatty acids that are otherwise insoluble in circulating plasma. While the crystal structure of human serum albumin (HSA) as well as its binding with fatty acids has been characterized, the three dimensional structure of bovine serum albumin (BSA) has not been determined although both albumins share 76% sequence homology. In this study we used mass spectrometry coupled with chemical cross-linking, to probe the tertiary structure of BSA. BSA was modified with lysine specific cross-linkers, bis(sulfosuccinimidyl) suberate (BS 3 ), disuccinimidyl suberate (DSS) or disuccinimidyl glutarate (DSG), digested with trypsin and analyzed by tandem mass spectrometry. With O-18 labeling during the digestion, through-space cross-linked peptides were readily identified in mass spectra by a characteristic 8 Da shift. From the cross-linked peptides identified in this study, we found that 12 pairs of lysine residues were separated within 20 Å, while 5 pairs were spaced between 20 and 24 Å. The spatial distance constraints generated from five K-K pairs in BSA were consistent with the corresponding distance obtained from the crystal structure of HSA, although only six equivalent K-K pairs could be compared. According to our data, the distance between K235 of IIA and K374 of IIB domain in BSA was farther by 7-11 Å than that expected from the crystal structure of HSA, suggesting structural differences between BSA and HSA in this region. The distance constraints obtained for lysine residues using various cross-linkers should be valuable in assisting the determination of the 3-D structure of

show abstract

“…Chemical cross-linking of proteins with variable binding affinities provides a means of assaying critical contact sites (1)(2)(3)(4)(5)(6). For certain specialized cases, natural enzymatic activities may be exploited to serve as highly selective covalent stabilization.…”

mentioning

confidence: 99%