NORMAL GENOMIC

• Sinha K, Jen-Jacobson L, Rule GS
• Divide and conquer is always best: sensitivity of methyl correlation experiments.
• J Biomol NMR. 2013; 56: 331-5
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• The HMCM [CG]CBCA experiment (Tugarinov and Kay in J Am Chem Soc 125:13868-13878, 2003) correlates methyl carbon and proton shifts to Cgamma, Cbeta, and Calpha resonances for the purpose of resonance assignments. The relative sensitivity of the HMCM[CG]CBCA sequence experiment is compared to a divide-and-conquer approach to assess whether it is best to collect all of the methyl correlations at once, or to perform separate experiments for each correlation. A straightforward analysis shows that the divide-and-conquer approach is intrinsically more sensitive, and should always be used to obtain methyl-Cgamma, Cbeta, and Calpha correlations. The improvement in signal-to-noise associated with separate experiments is illustrated by the detection of methyl-aliphatic correlations in a 65 kDa protein-DNA complex.

• Wu C et al.
• (1)H, (13)C and (15)N backbone and side-chain resonance assignments of reduced CcmG from Escherichia coli.
• Biomol NMR Assign. 2013; 7: 105-8
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• CcmG is a periplasmic, membrane-anchored protein widely distributed in a variety of species. In Escherichia coli, the CcmG protein always acts as a weak reductant in the electron transport chain during cytochrome c maturation (Ccm). Here we report (1)H, (15)N and (13)C backbone and side-chain resonance assignments of the reduced CcmG protein (residues 19-185, renumbered as 1-167) from E. coli. This work lays the essential basis for the further structural and functional analysis of reduced CcmG.

• Shin JS, Kim KS, Ryu KS, Han K, Lee Y, Choi BS
• Structural analysis of Escherichia coli C5 protein.
• Proteins. 2012; 80: 963-7

• Renault M et al.
• Solid-state NMR spectroscopy on cellular preparations enhanced by dynamic nuclear polarization.
• Angew Chem Int Ed Engl. 2012; 51: 2998-3001

• Nakada S, Takahashi H, Sakakura M, Kurono M, Shimada I
• Backbone resonance assignments for the periplasmic chaperone LolA from Escherichia coli.
• Biomol NMR Assign. 2007; 1: 125-7
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• LolA is an essential periplasmic protein in Gram-negative bacteria and plays a role in transporting lipoproteins through periplasmic space from the inner to the outer membrane. We established backbone resonance assignments of 2H/13C/15N labeled LolA from Escherichia coli.

• Gossert AD, Hiller S, Fiorito F, Wuthrich K
• NMR assignment of the E. coli type 1 pilus protein FimF.
• J Biomol NMR. 2007; 38: 195-195

• Revington M, Semesi A, Yee A, Arrowsmith CH, Shaw GS
• The solution structure of the protein ydhA from Escherichia coli.
• J Biomol NMR. 2006; 35: 295-300

• Shivarattan T, Chen HA, Simpson P, Sedgwick B, Matthews S
• Resonance assignments of Escherichia coli AlkB: a key 2-oxoglutarate and Fe(II) dependent dioxygenase of the adaptive DNA-repair response.
• J Biomol NMR. 2005; 33: 138-138

• Song J, Zhao Q, Lee MS, Markley JL
• 1H, 15N and 13C resonance assignments of the putative Bet v 1 family protein At1g24000.1 from Arabidopsis thaliana.
• J Biomol NMR. 2005; 32: 335-335

• Feng Y, Rouhier N, Jacquot JP, Xia B
• 1H, 15N, and 13C resonance assignments of reduced glutaredoxin C1 from Populus tremula x tremuloides.
• J Biomol NMR. 2005; 31: 263-4

• Lohr F, Rogov VV, Shi M, Bernhard F, Dotsch V
• Triple-resonance methods for complete resonance assignment of aromatic protons and directly bound heteronuclei in histidine and tryptophan residues.
• J Biomol NMR. 2005; 32: 309-28
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• A set of three experiments is described which correlate aromatic resonances of histidine and tryptophan residues with amide resonances in 13C/15N-labelled proteins. Provided that backbone 1H and 15N positions of the sequentially following residues are known, this results in sequence-specific assignment of histidine 1H(delta2)/13C(delta2) and 1H(epsilon1)/13C(epsilon1) as well as tryptophan 1H(delta1)/13C(delta1), 1H(zeta2)/13C(zeta2), 1H(eta2)/13C(eta2), 1H(epsilon3)/13C(epsilon3), 1H(zeta3)/13C(zeta3) and 1H(epsilon1)/15N(epsilon1) chemical shifts. In the reverse situation, these residues can be located in the 1H-(15)N correlation map to facilitate backbone assignments. It may be chosen between selective versions for either of the two amino acid types or simultaneous detection of both with complete discrimination against phenylalanine or tyrosine residues in each case. The linkages between delta-proton/carbon and the remaining aromatic as well as backbone resonances do not rely on through-space interactions, which may be ambiguous, but exclusively employ one-bond scalar couplings for magnetization transfer instead. Knowledge of these aromatic chemical shifts is the prerequisite for the analysis of NOESY spectra, the study of protein-ligand interactions involving histidine and tryptophan residues and the monitoring of imidazole protonation states during pH titrations. The new methods are demonstrated with five different proteins with molecular weights ranging from 11 to 28 kDa.

• Hong E, Shin J, Kang SW, Tanaka T, Lee W
• Resonance assignments and secondary structureof hPrxVI, a 25 kDa 1-cys human peroxiredoxin enzyme.
• J Biomol NMR. 2005; 31: 267-8

• Hemmi H et al.
• (1)H, (13)C, and (15)N chemical shift assignment of the C-terminal 15 kDa domain of a novel galactose-binding protein from the earthworm Lumbricus terrestris.
• J Biomol NMR. 2004; 30: 377-8

• Eisenmann A, Schwarz S, Rosch P, Schweimer K
• Sequence-specific 1H, 13C, 15N resonance assignments and secondary structure of the carboxyterminal domain of the E. coli transcription factor NusA.
• J Biomol NMR. 2004; 28: 193-4

• Merkley N, Shaw GS
• Assignment of the (1)H, (13)C and (15)N resonances of the class II E2 conjugating enzyme, Ubc1.
• J Biomol NMR. 2004; 30: 369-70

• Ukpabi N, Sharma S, Spaller MR, Tsang P
• (1)H, (15)N and (13)C backbone and side chain assignments of PSD-95 PDZ3 protein.
• J Biomol NMR. 2004; 30: 111-2

• Kostic M, Pochapsky TC
• (1)H, (13)C and (15)N chemical shift assignments of an enolase-phosphatase, E1, from Klebsiella oxytoca.
• J Biomol NMR. 2004; 30: 359-60

• Sugimori N, Torizawa T, Aceti DJ, Thao S, Markley JL, Kainosho M
• (1)H, (13)C and (15)N backbone assignment of a 32 kDa hypothetical protein from Arabidopsis thaliana, At3g16450.1.
• J Biomol NMR. 2004; 30: 357-8

• Charier G et al.
• 1H, 13C and 15N resonance assignments of the region 1463-1617 of the mouse p53 binding protein 1 (53BP1).
• J Biomol NMR. 2004; 28: 303-4

• Takinowaki H, Matsuda Y, Yoshida T, Kobayashi Y, Ohkubo T
• 1H, 13C and 15N resonance assignments of the N-terminal 16 kDa domain of Escherichia coli Ada protein.
• J Biomol NMR. 2004; 29: 447-8

• Marulanda D, Tasayco ML, McDermott A, Cataldi M, Arriaran V, Polenova T
• Magic angle spinning solid-state NMR spectroscopy for structural studies of protein interfaces. resonance assignments of differentially enriched Escherichia coli thioredoxin reassembled by fragment complementation.
• J Am Chem Soc. 2004; 126: 16608-20
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• De novo site-specific backbone and side-chain resonance assignments are presented for U-15N(1-73)/U-13C,15N(74-108) reassembly of Escherichia coli thioredoxin by fragment complementation, determined using solid-state magic angle spinning NMR spectroscopy at 17.6 T. Backbone dihedral angles and secondary structure predicted from the statistical analysis of 13C and 15N chemical shifts are in general agreement with solution values for the intact full-length thioredoxin, confirming that the secondary structure is retained in the reassembled complex prepared as a poly(ethylene glycol) precipitate. The differential labeling of complementary thioredoxin fragments introduced in this work is expected to be beneficial for high-resolution structural studies of protein interfaces formed by protein assemblies by solid-state NMR spectroscopy.

• Schedlbauer A et al.
• Sequence-specific resonance assignments of ICln, an ion channel cloned from epithelial cells.
• J Biomol NMR. 2003; 27: 399-400

• Bugg TD, Fleming SM, Robertson TA, Langley GJ
• 2-hydroxy-6-keto-nona-2,4-diene 1,9-dioic acid 5,6-hydrolase: evidence from 18O isotope exchange for gem-diol intermediate.
• Methods Enzymol. 2002; 354: 106-18

• Swapna GV et al.
• Resonance assignments for cold-shock protein ribosome-binding factor A (RbfA) from Escherichia coli.
• J Biomol NMR. 2001; 21: 389-90

• Miron S, Borza T, Saveanu C, Gilles AM, Barzu O, Craescu CT
• 1H, 13C and 15N resonance assignment of YajQ, a protein of unknown structure and function from Escherichia coli.
• J Biomol NMR. 2001; 20: 287-8