Herman J. C. Berendsen, a Very Modest Genius.

This letter gives a description of my interactions with Herman over more than 30 years. His teaching, his tremendous insight in subjects newly presented to him, his generousness, his playful interactions with colleagues and students, the freedom in research direction that he allowed and also expected from his PhD students.

Construction and performance of an NMR tube with a sample cavity formed within magnetic susceptibility-matched glass.

We describe the construction and performance of an NMR tube with a magnetic susceptibility matched sample cavity that confines the solution within the detection zone in the axial direction and in a quasi-rectangular region in the radial direction. The slot-like sample cavity provides both good sample volume efficiency and tolerance to sensitivity loss in the sample space. The signal-to-noise ratio per unit volume of the constructed tube was 2.

Direct NMR detection of the binding of functional ligands to the human sweet receptor, a heterodimeric family 3 GPCR.

We present a robust method for monitoring the binding of ligands to the heterodimeric (T1R2+T1R3) human sweet receptor (a family 3 GPCR receptor). The approach utilizes saturation transfer difference (STD) NMR spectroscopy with receptor proteins expressed on the surface of human epithelial kidney cells. The preparation investigated by NMR can contain either live cells or membranes isolated from these cells containing the receptor.

Carbonyl carbon label selective (CCLS) 1H-15N HSQC experiment for improved detection of backbone 13C-15N cross peaks in larger proteins.

We present a highly sensitive pulse sequence, carbonyl carbon label selective (1)H-(15)N HSQC (CCLS-HSQC) for the detection of signals from (1)H-(15)N units involved in (13)C'-(15)N linkages. The CCLS-HSQC pulse sequence utilizes a modified (15)N CT evolution period equal to 1/( [Formula: see text]) ( approximately 33 ms) to select for (13)C'-(15)N pairs. By collecting CCLS-HSQC and HNCO data for two proteins (8 kDa ubiquitin and 20 kDa HscB) at various temperatures (5-40 degrees C) in order to vary correlation times, we demonstrate the superiority of the CCLS-HSQC pulse sequence for proteins with long correlation times (i.

Structural insight into the self-sacrifice mechanism of enediyne resistance.

The recent discovery of the first "self-sacrifice" mechanism for bacterial resistance to the enediyne antitumor antibiotics, where enediyne-induced proteolysis of the resistance protein CalC inactivates both the highly reactive metabolite and the resistance protein, revealed yet another ingenious bacterial mechanism for controlling reactive metabolites. As reported herein, the first 3D structures of CalC and CalC in complex with calicheamicin (CLM) divulge CalC to be a member of the steroidogenic acute regulatory protein (StAR)-related transfer (START) domain superfamily. In contrast to previous studies of proteins known to bind DNA-damaging natural products ( e.

Solution structure of the low-molecular-weight protein tyrosine phosphatase from Tritrichomonas foetus reveals a flexible phosphate binding loop.

Eukaryotic low-molecular-weight protein tyrosine phosphatases (LMW PTPs) contain a conserved serine, a histidine with an elevated pKa, and an active site asparagine that together form a highly conserved hydrogen bonding network. This network stabilizes the active site phosphate binding loop for optimal substrate binding and catalysis. In the phosphatase from the bovine parasite Tritrichomonas foetus (TPTP), both the conserved serine (S37) and asparagine (N14) are present, but the conserved histidine has been replaced by a glutamine residue (Q67).

High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection.

We describe a novel approach to the rapid collection and processing of multidimensional NMR data: "high-resolution iterative frequency identification for NMR" (HIFI-NMR). As with other reduced dimensionality approaches, HIFI-NMR collects n-dimensional data as a set of two-dimensional (2D) planes. The HIFI-NMR algorithm incorporates several innovative features.

Preparation, physical properties, on-bead binding assay and spectroscopic reliability of 25 barcoded polystyrene-poly(ethylene glycol) graft copolymers.

Here we describe the preparation of 25 beaded polystyrene-poly(ethylene glycol) graft copolymers from six spectroscopically active styrene monomers: styrene, 2,5-dimethylstyrene, 4-methylstyrene, 2,4-dimethylstyrene, 4-tert-butylstyrene, and 3-methylstyrene. These polymers were thoroughly characterized by Raman, infrared, and (1)H/(13)C NMR spectroscopies, and differential scanning calorimetry. Determination of the swelling properties, peptide synthesis, and on-bead streptavidin-alkaline phosphatase (SAP) binding assay further established that their physical and chemical properties where not significantly altered by the diversity of their encoded polystyrene core.

Multiple conformations of NAD and NADH when bound to human cytosolic and mitochondrial aldehyde dehydrogenase.

Crystallographic analysis revealed that the nicotinamide ring of NAD can bind with multiconformations to aldehyde dehydrogenase (ALDH) (Ni, L., Zhou, J., Hurley, T.

Entropically driven self-assembly of multichannel rosette nanotubes.

Rosette nanotubes are a new class of organic nanotubes obtained through the hierarchical self-assembly of low molecular weight synthetic modules in water. Here we demonstrate that these materials can serve as scaffolds for the supramolecular synthesis of multichannel nanotubular architectures and report on the discovery of their entropy-driven self-assembly process.

A thermophilic mini-chaperonin contains a conserved polypeptide-binding surface: combined crystallographic and NMR studies of the GroEL apical domain with implications for substrate interactions.

A homologue of the Escherichia coli GroEL apical domain was obtained from thermophilic eubacterium Thermus thermophilus. The domains share 70 % sequence identity (101 out of 145 residues). The thermal stability of the T.

RNA recognition by a bent alpha-helix regulates transcriptional antitermination in phage lambda.

A novel RNA recognition motif is characterized in an arginine-rich peptide. The motif, derived from lambda transcriptional antitermination protein N, regulates an RNA-directed genetic switch. Its characterization by multidimensional nuclear magnetic resonance (NMR) demonstrates specific RNA-dependent folding of N- and C-terminal recognition helices separated by a central bend.

An RNA enhancer in a phage transcriptional antitermination complex functions as a structural switch.

Antitermination protein N regulates the transcriptional program of phage lambda through recognition of RNA enhancer elements. Binding of an arginine-rich peptide to one face of an RNA hairpin organizes the other, which in turn binds to the host antitermination complex. The induced RNA structure mimics a GNRA hairpin, an organizational element of rRNA and ribozymes.

A (13)C double-filtered NOESY with strongly reduced artefacts and improved sensitivity.

A (1)H NOESY experiment with two (13)C half-filters is described which has, compared to previously reported versions, an enhanced overall sensitivity and strongly reduced intramolecular cross peaks in any part of the spectrum edited for intermolecular NOEs. By adding a shaped (13)C pulse to the half-filter which selectively inverts the aromatic resonances, the filter can be tuned separately and simultaneously for the aliphatic and aromatic regions. Contrary to recently proposed schemes, no magnetization is destroyed, so that full sensitivity is retained for symmetric systems such as homodimers.

NMR structure determination of tick anticoagulant peptide (TAP).

Tick anticoagulant peptide (TAP) is a potent and selective 60-amino acid inhibitor of the serine protease Factor Xa (fXa), the penultimate enzyme in the blood coagulation cascade. The structural features of TAP responsible for its remarkable specificity for fXa are unknown, but the binding to its target appears to be unique. The elucidation of the TAP structure may facilitate our understanding of this new mode of serine protease inhibition and could provide a basis for the design of novel fXa inhibitors.

A constant-time (13)C- (1)H HSQC with uniform excitation over the complete (13)C chemical shift range.

An improved version of the constant-time HSQC experiment is presented that gives uniform sensitivity over the complete (13)C bandwidth in (13)C-(1)H correlation experiments without creating artifacts in the methyl and aromatic regions of the spectra. The improvement is achieved by replacing the refocussing (13)C 180° pulse in the evolution time by a combination of a full-power (22 kHz) hyperbolic secant 180° pulse that inverts and refocusses the entire (13)C window, immediately followed by a selective 180° pulse on the CO region. Further improvement in signal-to-noise in the aromatic and methyl regions, although less spectacular, is obtained by replacing the other two 180° (13)C pulses in the INEPT parts of the pulse sequence by full-power hyperbolic secant pulses.

Conformational properties of four peptides corresponding to alpha-helical regions of Rhodospirillum cytochrome c2 and bovine calcium binding protein.

Four peptides corresponding to alpha-helical regions delimited by residues 63-73 and 97-112 of cytochrome c2 (Rhodospirillum) and residues 24-36 and 45-55 of bovine calcium binding protein are predicted to be alpha-helical by a recently developed method [Rooman, M., Kocher, J.P.

Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: full assignment, tertiary structure, and comparison with the globular domain of histone H5.

The globular domain of chicken histone H1 (GH1) has been studied by 1H homonuclear and 1H-15N heteronuclear 2D NMR spectroscopy. After the full assignment of the proton and 15N resonances, the tertiary structure of GH1 was determined by an iterative procedure using distance geometry and restrained simulated annealing. The secondary structure elements of GH1, three helices (S5-A16, S24-A34, N42-K56) followed by a beta-hairpin (L59-L73), are folded in a manner very similar to the corresponding parts of the globular domain of chicken histone H5 (GH5) [Clore et al.

Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: sequential assignment and secondary structure.

A recombinant 75 amino acid polypeptide corresponding to the globular domain of the chicken histone H1 (GH1) has been studied by 1H homonuclear and 1H-15N heteronuclear 2D NMR spectroscopy. Sequential assignment of the backbone and beta-proton resonances has enabled us to determine the secondary structure of GH1. It was found to consist of three helical regions (T7-S17, L25-Y37, E40-K56) and probably a beta-hairpin (L59-L73).

Transfer nuclear Overhauser effect study of the conformation of oxytocin bound to bovine neurophysin I.

This study reports the structure of the peptide hormone oxytocin bound to its carrier protein, neurophysin I, obtained by nuclear magnetic resonance techniques. At the pH value of 2.1 in our experiments, the ligand is in fast exchange with its carrier protein, allowing the use of transfer-NOE methods.

Dual anomeric specificity and dual anomerase activity of phosphoglucoisomerase quantified by two-dimensional phase-sensitive 13C EXSY NMR.

The reversible conversion between D-glucose 6-phosphate and D-fructose 6-phosphate catalyzed by yeast phosphoglucoisomerase was studied by phase sensitive two-dimensional 13C-[1H] EXSY NMR spectroscopy at 150.869 and 125.759 MHz, using 13C-enriched substrates in the C2 position of the D-hexose 6-phosphates.

Histidine-40 of ribonuclease T1 acts as base catalyst when the true catalytic base, glutamic acid-58, is replaced by alanine.

Mechanisms for the ribonuclease T1 (RNase T1; EC 3.1.27.

The complete structure of the trifoliin A lectin-binding capsular polysaccharide of Rhizobium trifolii 843.

The complete structure of the acidic, extracellular, capsular polysaccharide of Rhizobium trifolii 843 has been elucidated by a combination of chemical, enzymic, and spectroscopic methods, confirming an earlier proposed sugar sequence and assigning the locations of the acyl substituents. The polysaccharide was depolymerized by a lyase into octasaccharide units which were uniform in carbohydrate composition and linkage. These units also contained a uniform distribution of acetyl and pyruvic acetal [O-(1-carboxyethylidene)] groups, and half of them were further acylated with D-3-hydroxybutanoyl groups.