New York-Structural GenomiX Research Consortium (NYSGXRC): A Large Scale Center for the Protein Structure Initiative

Bonanno, J.B.; Almo, Steven C.; Bresnick, Anne R.; Chance, Mark R.; Fiser, András; Swaminathan, Subramanyam; Jiang, Jiansheng; Studier, F. William; Shapiro, Lawrence; Lima, Christopher D.; Gaasterland, Theresa M.; Šali, Andrej; Bain, K.T.; Feil, I.; Gao, Xia; Lorimer, Don; Ramos, Aurora; Sauder, J.M.; Wasserman, Steven R.; Emtage, Spencer; D’Amico, K. L.; Burley, S.K.

doi:10.1007/s10969-005-6827-0

Cited by 54 publications

(54 citation statements)

References 6 publications

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“…Worse, for the ten sequence positions listed in Table 2, the percentage of partial occupancy of S versus Se seems to be different in each residue. This is an indication of possibility, that the investigated protein 3B40 [18], was not fully SeMet derivatized. Both refinement paths A and B, carried out in this work, did not allow answering the question what atom type, Se or S, is correct in the refined structure.…”

Section: Handling Of Two Different Atom Types Se and S In Refinemenmentioning

confidence: 89%

“…The publicly available, from the Protein Data Bank, entry 3B40 [18], which is under extensive investigation in this work, is most likely an example of that case. The partial presence of S-Met residues, or, in other words, not complete Se-Met derivatization of the protein, is possible [15].…”

Section: Handling Of Two Different Atom Types Se and S In Refinemenmentioning

confidence: 99%

“…The B-values obtained of both refinement paths A and B, are collected in Table 2. Table 2: Atomic displacement parameters (B-factors, Å2) and occupancies for the S and Se atoms in re-refinement of the PDB entry 3B40 [18]. Path A: refined B-factors, the presence of 100% sulfur was assumed.…”

Section: Handling Of Two Different Atom Types Se and S In Refinemenmentioning

confidence: 99%

“…The example of such inconsistence is the PDB entry 3B40 [18], which contains the following statement: 'SeMet modeled as Met' (see remark 3, other refinement remarks in the PDB file, or refine. details in cif file).…”

Section: Introductionmentioning

confidence: 99%

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Handling of Selenomethionines in Macromolecular Refinement

Błaszczyk¹

2014

Biochem Anal Biochem

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In the Protein Data Bank, we can find X-ray structures which were determined from selenium-derivatized proteins, but the deposited coordinates, to our surprise, contain native methionines. The problem is likely due to not complete substitution of native methionines with selenomethionines during chemical reaction. When the crystal grows from such sample, and later is subjected for X-ray analysis, it may show partial presence of native sulfur. This paper is a voice in discussion how to handle the refinement of selenomethionines. The purpose of this work is to explain why selenomethionines can't be refined purely as native methionines, particularly in macromolecular structures determined at high resolution. It is important because selenium and sulfur are different chemical elements. To explain the importance of refinement of correct atom type, author provides evidence, collected mainly from his previously reported small organic structures containing sulfur or selenium. Author emphasizes that the Xray structures, which contain selenium, are never identical with their sulfur-containing analogs. They differ at least in the respective bond lengths. Two available publicly X-ray structures have been re-refined, one small molecule and one macromolecule, in which the atom type was intentionally changed. Refinement of chemically incorrect atom type yielded non-natural behavior of atomic displacement parameters. Author concludes that the structures which contain incorrect atom types can't represent the experimental data but can serve only as models. There are examples, in the PDB, which show that selenomethionines in not fully Se-Met derivatized proteins can be refined with arbitrarily assumed fractional, less than 100%, occupancies. This inspired the author to perform various re-refinements, of the above mentioned Se-Met structure that contained S atoms in coordinates. In these re-refinements, selenomethionines are handled in different manners, and the results are compared. Author suggests refinement of chemical identities, selenium and sulfur, with fractional occupancies, as a method.

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Section: Handling Of Two Different Atom Types Se and S In Refinemenmentioning

confidence: 89%

Section: Handling Of Two Different Atom Types Se and S In Refinemenmentioning

confidence: 99%

Section: Handling Of Two Different Atom Types Se and S In Refinemenmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Handling of Selenomethionines in Macromolecular Refinement

Błaszczyk¹

2014

Biochem Anal Biochem

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“…The Protein Structure Database (PDB) currently contains ~2,200 proteins of unknown function [27]. These proteins tend to be "orphaned" from any further functional analysis because of a complete absence of information to guide a research project [28][29][30][31]. These orphaned proteins are ideal targets for analysis by FAST-NMR.…”

Section: The Fast-nmr Methodsmentioning

confidence: 99%

The application of FAST-NMR for the identification of novel drug discovery targets

Powers

Mercier

Copeland

2008

Drug Discovery Today

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Protein Characterisation in Proteomics

Meri

Baumann

2012

Encyclopedia of Life Sciences

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Proteomics refers to the comprehensive analysis of proteomes – the protein content of complex biological mixtures, that is, a whole proteome of a cell, microbe or a proteome of a certain tissue or just the proteome of the blood, saliva or cerebrospinal fluid. The aim is to separate and identify all the proteins of the chosen proteome and then to determine their interactome and with that their biological relevance and activity in that system at the moment of sample collection. Currently, such analyses would also include the characterisation of possible secondary modifications and determining the expression level of each protein. All this is performed by high‐end mass spectrometers that allow the identification and parallel quantification of several hundred proteins and several of their secondary modifications (e.g. phosphorylations, sumoylations, glycosylations etc .) in one analysis step. Thus, a big challenge is also to be able to deal with an enormous amount of complex data in order to make any sense of the results at the end. In this article, the authors will highlight some key issues for such analyses and describe some of the used technologies in greater detail. Key Concepts: Proteins are one of the key elements of life. Proteome is the full content of proteins in a given biological sample. Proteome content can change dynamically according to, for example, time, location and environmental conditions. Meaningful results from proteomic analysis can be obtained if the analysis is restricted to a well‐defined and targeted goal. Main methods include two‐dimensional gel separation, enzyme digestion and multidimensional liquid chromatography mass spectrometry. Along the flow of proteomic analysis it is important to choose the most appropriate approach (top‐down vs. bottom‐up, focused vs. broad, quantitative vs. qualitative, comparative, selective). Protein analysis can be subjected to positive and negative selection procedures for desired features. Post‐translational modifications can change protein characteristics and function. Large depositories of data are available for comparative analysis.

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New York-Structural GenomiX Research Consortium (NYSGXRC): A Large Scale Center for the Protein Structure Initiative

Cited by 54 publications

References 6 publications

Handling of Selenomethionines in Macromolecular Refinement

Handling of Selenomethionines in Macromolecular Refinement

The application of FAST-NMR for the identification of novel drug discovery targets

Protein Characterisation in Proteomics

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