Theoretical framework for NMR residual dipolar couplings in unfolded proteins.

abstract：:Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion ...

journal_title：Journal of biomolecular NMR

authors： Piai A,Gonnelli L,Felli IC,Pierattelli R,Kazimierczuk K,Grudziąż K,Koźmiński W,Zawadzka-Kazimierczuk A

更新日期：2016-03-01 00:00:00

abstract：:Characterization of the structure and dynamics of nucleic acids by NMR benefits significantly from position specifically labeled nucleotides. Here an E. coli strain deficient in the transketolase gene (tktA) and grown on glucose that is labeled at different carbon sites is shown to facilitate cost-effective and large ...

journal_title：Journal of biomolecular NMR

authors： Thakur CS,Luo Y,Chen B,Eldho NV,Dayie TK

更新日期：2012-02-01 00:00:00

abstract：:Many regulatory RNAs undergo dynamic exchanges that are crucial for their biological functions and NMR spectroscopy is a versatile tool for monitoring dynamic motions of biomolecules. Meaningful information on biomolecular dynamics requires an accurate measurement of relaxation parameters such as longitudinal (R1) rat...

journal_title：Journal of biomolecular NMR

authors： Nam H,Becette O,LeBlanc RM,Oh D,Case DA,Dayie TK

更新日期：2020-07-01 00:00:00

abstract：:Proton chemical shifts of a series of disordered linear peptides (H-Gly-Gly-X-Gly-Gly-OH, with X being one of the 20 naturally occurring amino acids) have been obtained using 1D and 2D 1H NMR at pH 5.0 as a function of temperature and solvent composition. The use of 2D methods has allowed some ambiguities in side-chai...

journal_title：Journal of biomolecular NMR

authors： Merutka G,Dyson HJ,Wright PE

更新日期：1995-01-01 00:00:00

abstract：:The efficiency of cell-free protein synthesis combined with combinatorial selective 15N-labelling provides a method for the rapid assignment of 15N-HSQC cross-peaks to the 19 different non-proline amino-acid types from five 15N-HSQC spectra. This strategy was explored with two different constructs of the C-terminal do...

journal_title：Journal of biomolecular NMR

authors： Wu PS,Ozawa K,Jergic S,Su XC,Dixon NE,Otting G

更新日期：2006-01-01 00:00:00

abstract：:Higher sensitivity of NMR spectrometers and novel isotopic labeling schemes have ushered the development of rapid data acquisition methodologies, improving the time resolution with which NMR data can be acquired. For nucleic acids, longitudinal relaxation optimization in conjunction with Ernst angle excitation (SOFAST...

journal_title：Journal of biomolecular NMR

authors： Sathyamoorthy B,Lee J,Kimsey I,Ganser LR,Al-Hashimi H

更新日期：2014-11-01 00:00:00

abstract：:The advantages of non-uniform sampling (NUS) in offering time savings and resolution enhancement in NMR experiments have been increasingly recognized. The possibility of sensitivity gain by NUS has also been demonstrated. Application of NUS to multidimensional NMR experiments requires the selection of a sampling schem...

journal_title：Journal of biomolecular NMR

authors： Sun S,Gill M,Li Y,Huang M,Byrd RA

更新日期：2015-05-01 00:00:00

abstract：:S3EPY is a Python extension to the program Sparky written to facilitate the assessment of coupling constants from in-phase/antiphase and spin-state-selective excitation (S(3)E) experiments. It enables the routine use of small scalar couplings by automating the coupling evaluation procedure. S3EPY provides an integrate...

journal_title：Journal of biomolecular NMR

authors： Novák P,Zídek L,Motácková V,Padrta P,Svenková A,Nuzillard JM,Krásný L,Sklenár V

更新日期：2010-02-01 00:00:00

abstract：:Lanthanide complexes based on the DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) cage are commonly used as phase contrast agents in magnetic resonance imaging, but can also be utilized in structural NMR applications due to their ability to induce either paramagnetic relaxation enhancement or a pseudoc...

journal_title：Journal of biomolecular NMR

authors： Strickland M,Schwieters CD,Göbl C,Opina AC,Strub MP,Swenson RE,Vasalatiy O,Tjandra N

更新日期：2016-10-01 00:00:00

abstract：:New base-type-edited transverse-relaxation optimized CT-HCN(C) experiments are presented that yield intra-base and sugar-to-base correlations for 13C-15N labeled RNA. High spectral resolution in the 13C and 15N dimensions is achieved by constant time (CT) frequency editing. A spectral editing filter applied during the...

journal_title：Journal of biomolecular NMR

authors： Van Melckebeke H,Pardi A,Boisbouvier J,Simorre JP,Brutscher B

更新日期：2005-08-01 00:00:00

abstract：:Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37% sequence homology with ...

journal_title：Journal of biomolecular NMR

authors： Hare BJ,Prestegard JH

更新日期：1994-01-01 00:00:00

abstract：:1H alpha, 13C alpha, and 15N alpha secondary shifts, defined as the difference between the observed value and the random coil value, have been calculated for interleukin-1 receptor antagonist protein and interleukin-1 beta. Averaging of the secondary chemical shifts with those of adjacent residues was used to smooth o...

journal_title：Journal of biomolecular NMR

authors： Stockman BJ,Scahill TA,Strakalaitis NA,Brunner DP,Yem AW,Deibel MR Jr

更新日期：1992-11-01 00:00:00

abstract：:The importance of protein chemical shift values for the determination of three-dimensional protein structure has increased in recent years because of the large databases of protein structures with assigned chemical shift data. These databases have allowed the investigation of the quantitative relationship between chem...

journal_title：Journal of biomolecular NMR

authors： Meiler J

更新日期：2003-05-01 00:00:00

abstract：:13CHD2 methyl isotopomers are particularly useful to study methyl dynamics in proteins because, as compared with other methyl isotopomers, the 13C relaxation mechanism for this isotopomer is straightforward. However, in the case of proteins, where (omega tau)2 > 1, the refocused INEPT pulse sequence does not completel...

journal_title：Journal of biomolecular NMR

authors： Ishima R,Louis JM,Torchia DA

更新日期：2001-10-01 00:00:00

abstract：:Calculated coupling constants (3JHNH alpha, 1JC alpha H alpha, 2JC'H alpha, 1JC alpha N and 2JC alpha N) from our accompanying paper [Edison, A.S. et al. (1994) J. Biomol. NMR, 4, 519-542] have been used to generate error surfaces that can provide estimates of the phi and psi angles in proteins. We have used experimen...

journal_title：Journal of biomolecular NMR

authors： Edison AS,Weinhold F,Westler WM,Markley JL

更新日期：1994-07-01 00:00:00

abstract：:The solution structure of the SH3 domain of human p56 Lck tyrosine kinase (Lck-SH3) has been determined by multidimensional heteronuclear NMR spectroscopy. The structure was calculated from a total of 935 experimental restraints comprising 785 distance restraints derived from 1017 assigned NOE cross peaks and 150 dihe...

journal_title：Journal of biomolecular NMR

authors： Hiroaki H,Klaus W,Senn H

更新日期：1996-09-01 00:00:00

abstract：:Pseudocontact shifts (PCS) induced by tags loaded with paramagnetic lanthanide ions provide powerful long-range structure information, provided the location of the metal ion relative to the target protein is known. Usually, the metal position is determined by fitting the magnetic susceptibility anisotropy (Δχ) tensor ...

journal_title：Journal of biomolecular NMR

authors： Abdelkader EH,Yao X,Feintuch A,Adams LA,Aurelio L,Graham B,Goldfarb D,Otting G

更新日期：2016-01-01 00:00:00

abstract：:NMR of macromolecules is limited by large transverse relaxation rates. In practice, this results in low efficiency of coherence transfer steps in multidimensional NMR experiments, leading to poor sensitivity and long acquisition times. The efficiency of coherence transfer can be maximized by design of relaxation optim...

journal_title：Journal of biomolecular NMR

authors： Frueh DP,Ito T,Li JS,Wagner G,Glaser SJ,Khaneja N

更新日期：2005-05-01 00:00:00

abstract：:Prerequisite for chemical shift (CS) and CS tensor calculations are highly refined structures defining the molecular surroundings of the nuclei under study. Here, we present geometry optimizations with 13C and 15N CS constraints for large bio-molecules like peptides and proteins. The method discussed here provides bot...

journal_title：Journal of biomolecular NMR

authors： Sternberg U,Witter R

更新日期：2019-12-01 00:00:00

abstract：:Under the condition that the longitudinal relaxation time of spin I is shorter than the longitudinal relaxation time of spin S the steady-state magnetization in [S,I]-TROSY-type experiments can be enhanced by intermediate storage of a part of the steady-state magnetization of spin I on spin S with a pulse sequence ele...

journal_title：Journal of biomolecular NMR

authors： Riek R

更新日期：2001-10-01 00:00:00

abstract：:Dynamics of large-amplitude conformational motions in proteins are complex and less understood, although these processes are intimately associated with structure, folding, stability, and function of proteins. Here, we use a large set of spectra obtained by cross-relaxation suppressed exchange NMR spectroscopy (EXSY) t...

journal_title：Journal of biomolecular NMR

authors： Rao DK,Bhuyan AK

更新日期：2007-11-01 00:00:00

abstract：:In this work, we show how the water flip-back approach that is widely employed in solution-state NMR can be adapted to proton-detected MAS solid-state NMR of highly deuterated proteins. The scheme allows to enhance the sensitivity of the experiment by decreasing the recovery time of the proton longitudinal magnetizati...

journal_title：Journal of biomolecular NMR

authors： Chevelkov V,Xiang S,Giller K,Becker S,Lange A,Reif B

更新日期：2015-02-01 00:00:00

abstract：:The development of new protein labeling strategies, along with optimized experiments that exploit the label, have significantly impacted on the types of biochemical problems that can now be addressed by solution NMR spectroscopy. Here we describe how methyl labeling of key residues in a highly deuterated protein backg...

journal_title：Journal of biomolecular NMR

authors： Ruschak AM,Kay LE

更新日期：2010-01-01 00:00:00

abstract：:An approach to the determination of the 2-(13)C' chemical shift (CS) tensor orientation in pyrimidine bases via heteronuclear MAS NMR spectroscopy is presented. Considering a dipolar coupled spin 1/2 network of the type S1-I-S2 consisting of directly bonded heteronuclear spins, we have carried out numerical simulation...

journal_title：Journal of biomolecular NMR

authors： Leppert J,Heise B,Ramachandran R

更新日期：2000-10-01 00:00:00

abstract：:Based on high-resolution structures of the free molecules accurate determination of structures of protein complexes by NMR spectroscopy is possible using residual dipolar couplings. In order, however, to be able to apply these methods, protein backbone resonances have to be assigned first. This NMR assignment process ...

journal_title：Journal of biomolecular NMR

authors： Zweckstetter M

更新日期：2003-09-01 00:00:00

abstract：:We present reduced dimensionality (RD) 3D HN(CA)NH for efficient sequential assignment in proteins. The experiment correlates the (15)N and (1)H chemical shift of a residue ('i') with those of its immediate N-terminal (i - 1) and C-terminal (i + 1) neighbors and provides four-dimensional chemical shift correlations ra...

journal_title：Journal of biomolecular NMR

authors： Chandra K,Jaipuria G,Shet D,Atreya HS

更新日期：2012-02-01 00:00:00

abstract：:The biological environment in which a protein performs its function is a crowded milieu containing millions of molecules that can potentially lead to a great many transient, non-specific interactions. NMR spectroscopy is especially well suited to study these weak molecular contacts. Here, non-specific interactions bet...

journal_title：Journal of biomolecular NMR

authors： Latham MP,Kay LE

更新日期：2013-03-01 00:00:00

abstract：:Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing (15)N, (13)C' and (1)H(N) spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially (15)N and (13)C' spin...

journal_title：Journal of biomolecular NMR

authors： Mäntylahti S,Hellman M,Permi P

更新日期：2011-02-01 00:00:00

abstract：:Two new techniques offering considerable improvements in the quality of 1H photo-CIDNP spectra of proteins are demonstrated. Both focus on the problem of progressive photo-degradation of the flavin dye used to generate polarization in exposed tryptophan, tyrosine and histidine side-chains. One approach uses rapid addi...

journal_title：Journal of biomolecular NMR

authors： Maeda K,Lyon CE,Lopez JJ,Cemazar M,Dobson CM,Hore PJ

更新日期：2000-03-01 00:00:00

abstract：:The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation. of the anisotropic paramagnetic susceptibility tensor in the molecular frame whic...

journal_title：Journal of biomolecular NMR

authors： Xia Z,Nguyen BD,La Mar GN

更新日期：2000-06-01 00:00:00