The Re-referenced Protein Chemical shift Database (RefDB)
is an
NMR spectroscopy
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique based on re-orientation of atomic nuclei with non-zero nuclear spins in an external magnetic f ...
database of carefully corrected or re-referenced
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
s, derived from the BioMagResBank (BMRB) (Fig. 1). The database was assembled by using a structure-based
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
calculation program (called SHIFTX) to calculate expected
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
(1)H, (13)C and (15)N
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
s from
X-ray
An X-ray (also known in many languages as Röntgen radiation) is a form of high-energy electromagnetic radiation with a wavelength shorter than those of ultraviolet rays and longer than those of gamma rays. Roughly, X-rays have a wavelength ran ...
or
NMR
Nuclear magnetic resonance (NMR) is a physical phenomenon in which atomic nucleus, nuclei in a strong constant magnetic field are disturbed by a weak oscillating magnetic field (in the near and far field, near field) and respond by producing ...
coordinate data of previously assigned proteins reported in the BMRB. The comparison is automatically performed by a program called
SHIFTCOR
SHIFTCOR (Shift Correction) is a freely available web server as well as a stand-alone computer program for protein chemical shift re-referencing. Chemical shift referencing is a particularly widespread problem in biomolecular NMR with up to 25% ...
. The RefDB database currently provides reference-corrected
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
data on more than 2000 assigned
peptide
Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty am ...
s and
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s. Data from the database indicates that nearly 25% of BMRB entries with (13)C
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
assignments and 27% of BMRB entries with (15)N
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
assignments require significant
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
reference readjustments. Additionally, nearly 40% of
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
entries deposited in the BioMagResBank appear to have at least one assignment error. Users may download, search or browse the database through a number of methods available through the RefDB website. RefDB provides a standard
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
resource for biomolecular NMR spectroscopists, wishing to derive or compute
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
trends in
peptide
Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty am ...
s and
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s.
Scope and Access
All data in RefDB is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. RefDB data is available through a public web interface and downloads.
Features
All
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
s in RefDB have been computationally re-referenced to DSS (a common NMR
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
standard).
RefDB is a continuously updated resource that uses web-bots to query public databases (BMRB,
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a par ...
,
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...
) and fetch assignment, sequence and structure data on a weekly basis. It then applies a series of data checking routines (using keywords to remove paramagnetic or denatured proteins) followed by a series of calculations to identify and correct
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
referencing errors. RefDB is fully web-enabled database, it stores data in two standard formats (
NMR-STAR NMR-STAR is an extension of the STAR file format to store the results of biological NMR experiments.
Chemical file formats
{{chem-software-stub ...
and Shifty), it performs automated data updating, checking and validation and it provides open access to output data in a fully downloadable flat file format as well as in a hyperlinked browsable table (see Fig. 2). RefDB also supports keyword queries and sequence searches (using local
BLAST
Blast or The Blast may refer to:
*Explosion, a rapid increase in volume and release of energy in an extreme manner
*Detonation, an exothermic front accelerating through a medium that eventually drives a shock front
*A planned explosion in a mine, ...
). RefDB is usually updated on a weekly basis. The RefDB database, along with its associated software, is freely available at http://refdb.wishartlab.com and at the BMRB website.
Protocols
RefDB has been prepared using a combination of three different computer programs. The first program (SHIFTX) calculates
backbone
The spinal column, also known as the vertebral column, spine or backbone, is the core part of the axial skeleton in vertebrates. The vertebral column is the defining and eponymous characteristic of the vertebrate. The spinal column is a segmente ...
1H, 13C and 15N
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
s from protein 3D coordinate data. The second program (
SHIFTCOR
SHIFTCOR (Shift Correction) is a freely available web server as well as a stand-alone computer program for protein chemical shift re-referencing. Chemical shift referencing is a particularly widespread problem in biomolecular NMR with up to 25% ...
) compares the calculated shifts with the observed shifts, evaluates any statistically significant differences and performs the necessary chemical shift corrections. The third program (UPDATE) automatically retrieves newly deposited BMRB data along with any corresponding PDB data. UPDATE also directs the data to
SHIFTCOR
SHIFTCOR (Shift Correction) is a freely available web server as well as a stand-alone computer program for protein chemical shift re-referencing. Chemical shift referencing is a particularly widespread problem in biomolecular NMR with up to 25% ...
and appends the ‘corrected’ chemical shift file to the RefDB database.
What RefDB provides
*A downloadable database of 2162 re-referenced protein
chemical shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
files
*A comprehensive list of BMRB and re-referenced BMRB entries with corresponding PDB entries (See Fig. 2)
*A tab-delimited summary of all RefDB entries
*Secondary structure information for each protein sequence in shifty format
*Statistical information
**Referencing errors (in ppm) for backbone atoms
**Averaged backbone chemical shift values for secondary structure assignments (Alpha-helix, beta and coil)
See also
*
Chemical Shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
*
SHIFTCOR
SHIFTCOR (Shift Correction) is a freely available web server as well as a stand-alone computer program for protein chemical shift re-referencing. Chemical shift referencing is a particularly widespread problem in biomolecular NMR with up to 25% ...
*
Protein structure database
In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the ...
*
Protein Chemical Shift Re-Referencing
*
Protein secondary structure
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occu ...
*
Protein Chemical Shift Prediction
*
Chemical shift index
The chemical shift index or CSI is a widely employed technique in protein nuclear magnetic resonance spectroscopy that can be used to display and identify the location (i.e. start and end) as well as the type of protein secondary structure (beta ...
*
Protein NMR
Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and ...
References
General References
*
*
*{{cite journal , title=Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications, last=Wang, first=L, author2=Eghbalnia HR , author3=Bahrami A , author4=Markley JL , journal=Journal of Biomolecular NMR, date=May 2005, volume=32, issue=1, pages=13–22, pmid= 16041479 , doi=10.1007/s10858-005-1717-0, s2cid=33690078
Chemical databases
Nuclear magnetic resonance software
Protein methods
Chemistry software
Biological databases