NMR resonance assignments for sparsely 15N labeled proteins. 2007

Lianmei Feng, and Han-Seung Lee, and James H Prestegard
Complex Carbohydrate Research Center, University of Geogia, Athens, GA 30602-4712, USA.

For larger proteins, and proteins not amenable to expression in bacterial hosts, it is difficult to deduce structures using NMR methods based on uniform (13)C, (15)N isotopic labeling and observation of just nuclear Overhauser effects (NOEs). In these cases, sparse labeling with selected (15)N enriched amino acids and extraction of a wider variety of backbone-centered structural constraints is providing an alternate approach. A limitation, however, is the absence of resonance assignment strategies that work without uniform (15)N, (13)C labeling or preparation of numerous samples labeled with pairs of isotopically labeled amino acids. In this paper an approach applicable to a single sample prepared with sparse (15)N labeling in selected amino acids is presented. It relies on correlation of amide proton exchange rates, measured from data on the intact protein and on digested and sequenced peptides. Application is illustrated using the carbohydrate binding protein, Galectin-3. Limitations and future applications are discussed.

UI MeSH Term Description Entries
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D009584 Nitrogen An element with the atomic symbol N, atomic number 7, and atomic weight [14.00643; 14.00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth's atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells.
D009587 Nitrogen Isotopes Stable nitrogen atoms that have the same atomic number as the element nitrogen but differ in atomic weight. N-15 is a stable nitrogen isotope. Nitrogen Isotope,Isotope, Nitrogen,Isotopes, Nitrogen
D010455 Peptides Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are considered to be larger versions of peptides that can form into complex structures such as ENZYMES and RECEPTORS. Peptide,Polypeptide,Polypeptides
D010649 Phenylalanine An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE. Endorphenyl,L-Phenylalanine,Phenylalanine, L-Isomer,L-Isomer Phenylalanine,Phenylalanine, L Isomer
D011522 Protons Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion. Hydrogen Ions,Hydrogen Ion,Ion, Hydrogen,Ions, Hydrogen,Proton
D003903 Deuterium The stable isotope of hydrogen. It has one neutron and one proton in the nucleus. Deuterons,Hydrogen-2,Hydrogen 2
D000577 Amides Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed) Amide
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D017434 Protein Structure, Tertiary The level of protein structure in which combinations of secondary protein structures (ALPHA HELICES; BETA SHEETS; loop regions, and AMINO ACID MOTIFS) pack together to form folded shapes. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Tertiary Protein Structure,Protein Structures, Tertiary,Tertiary Protein Structures

Related Publications

Lianmei Feng, and Han-Seung Lee, and James H Prestegard
April 2017, Journal of biomolecular NMR,
Lianmei Feng, and Han-Seung Lee, and James H Prestegard
April 2009, Journal of the American Chemical Society,
Lianmei Feng, and Han-Seung Lee, and James H Prestegard
January 2002, Journal of magnetic resonance (San Diego, Calif. : 1997),
Lianmei Feng, and Han-Seung Lee, and James H Prestegard
December 2022, Journal of magnetic resonance (San Diego, Calif. : 1997),
Lianmei Feng, and Han-Seung Lee, and James H Prestegard
May 2019, Journal of molecular biology,
Lianmei Feng, and Han-Seung Lee, and James H Prestegard
October 1996, Journal of biomolecular NMR,
Lianmei Feng, and Han-Seung Lee, and James H Prestegard
September 2005, IUBMB life,
Lianmei Feng, and Han-Seung Lee, and James H Prestegard
April 2001, Journal of biomolecular NMR,
Lianmei Feng, and Han-Seung Lee, and James H Prestegard
February 2000, Journal of biomolecular NMR,
Lianmei Feng, and Han-Seung Lee, and James H Prestegard
January 1993, Journal of biomolecular NMR,
Copied contents to your clipboard!