For more than a decade, the Joint Center for Structural Genomics ( JCSG ; www.jcsg.org ) worked toward increased three‐dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high‐throughput ( HT ) structure determination centers of the Protein Structure Initiative ( PSI ; www.nigms.nih.gov/Research/specificareas/PSI ). To achieve the goals of the PSI , the JCSG made use of the complementarity of structure determination by X‐ray crystallography and nuclear magnetic resonance ( NMR ) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three‐dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG . There are five new folds, which were classified as domains of unknown functions ( DUF ), three of the proteins could be functionally annotated based on three‐dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank ( PDB ) and were classified as DUF s.

The outer membrane protein Ail (Adhesion invasion locus) is one of the most abundant proteins on the cell surface of Yersinia pestis during human infection. Its functions are expressed through interactions with a variety of human host proteins, and are essential for microbial virulence. Structures of Ail in micelles have been determined by X-ray diffraction and solution NMR spectroscopy, but those samples contained detergents that interfere with functionality, thus, precluding analysis of the structural basis for Ail's biological activity. Here, we present high-resolution magic angle spinning (MAS) solid-state NMR spectra of Ail in detergent-free phospholipid liposomes, prepared with a lipid to protein molar ratio of 100. The 13C-detected spectra enable resonance assignments for many nitrogen and carbon sites in the sequence of Ail, covering 80% of the transmembrane region. The 1H-detected 1H/15N correlation solid-state NMR spectra of Ail in liposomes compare very favorably with the solution NMR TROSY spectra of Ail in nanodiscs, prepared with a similar lipid to protein molar ratio. We also acquired high resolution 15N-detection solid state NMR spectra of Ail in magnetically aligned bicelles. These static spectra contain rich anisotropic information complementary to the MAS data. Furthermore, we studied the effect of lipopolysaccharide, a major component of the bacteria outer membrane, on the structure and dynamics of Ail in membranes. Altogether, the ability to acquire high resolution NMR data under both MAS and static conditions allows us to obtain structural information about this membrane protein in a near native environment and to probe protein dynamics on a wide range of time scale. NMR studies also provide molecular information about the functional interactions of Ail with its protein partners from human host cells, useful for the development of drugs targeting Ail.

The outer membrane protein Ail (Adhesion invasion locus) is one of the most abundant proteins on the cell surface of Yersinia pestis during human infection. Its functions are expressed through interactions with a variety of human host proteins, and are essential for microbial virulence. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but those samples contained detergents that interfere with functionality, thus, precluding analysis of the structural basis for Ail's biological activity. Here, we demonstrate that high-resolution solid-state NMR spectra can be obtained from samples of Ail in detergent-free phospholipid liposomes, prepared with a lipid to protein molar ratio of 100. The spectra, obtained with 13C or 1H detection, have very narrow line widths (0.40–0.60 ppm for 13C, 0.11–0.15 ppm for 1H, and 0.46–0.64 ppm for 15N) that are consistent with a high level of sample homogeneity. The spectra enable resonance assignments to be obtained for N, CO, CA and CB atomic sites from 75 out of 156 residues in the sequence of Ail, including 80% of the transmembrane region. The 1H-detected solid-state NMR 1H/15N correlation spectra obtained for Ail in liposomes compare very favorably with the solution NMR 1H/15N TROSY spectra obtained for Ail in nanodiscs prepared with a similar lipid to protein molar ratio. These results set the stage for studies of the molecular basis of the functional interactions of Ail with its protein partners from human host cells, as well as the development of drugs targeting Ail.

Yersinia pestis the causative agent of plague, is highly pathogenic and poses very high risk to public health. The outer membrane protein Ail (Adhesion invasion locus) is one of the most highly expressed proteins on the cell surface of Y. pestis, and a major target for the development of medical countermeasures. Ail is essential for microbial virulence and is critical for promoting the survival of Y. pestis in serum. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but the protein's activity is influenced by the detergents in these samples, underscoring the importance of the surrounding environment for structure-activity studies. Here we describe the backbone structure of Ail, determined in lipid bilayer nanodiscs, using solution NMR spectroscopy. We also present solid-state NMR data obtained for Ail in membranes containing lipopolysaccharide (LPS), a major component of the bacterial outer membranes. The protein in lipid bilayers, adopts the same eight-stranded β-barrel fold observed in the crystalline and micellar states. The membrane composition, however, appears to have a marked effect on protein dynamics, with LPS enhancing conformational order and slowing down the 15N transverse relaxation rate. The results provide information about the way in which an outer membrane protein inserts and functions in the bacterial membrane.

Multisite phosphorylation is required for the biological function of serine-arginine (SR) proteins, a family of essential regulators of mRNA splicing. These modifications are catalyzed by serine-arginine protein kinases (SRPKs) that phosphorylate numerous serines in arginine-serine-rich (RS) domains of SR proteins using a directional, C-to-N-terminal mechanism. The present studies explore how SRPKs govern this highly biased phosphorylation reaction and investigate biological roles of the observed directional phosphorylation mechanism. Using NMR spectroscopy with two separately expressed domains of SRSF1, we showed that several residues in the RNA-binding motif 2 interact with the N-terminal region of the RS domain (RS1). These contacts provide a structural framework that balances the activities of SRPK1 and the protein phosphatase PP1, thereby regulating the phosphoryl content of the RS domain. Disruption of the implicated intramolecular RNA-binding motif 2-RS domain interaction impairs both the directional phosphorylation mechanism and the nuclear translocation of SRSF1 demonstrating that the intrinsic phosphorylation bias is obligatory for SR protein biological function.

High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data.

Flavodoxins in combination with the flavin mononucleotide (FMN) cofactor play important roles for electron transport in prokaryotes. Here, novel insights into the FMN-binding mechanism to flavodoxins-4 were obtained from the NMR structures of the apo-protein from Lactobacillus acidophilus (YP_193882.1) and comparison of its complex with FMN. Extensive reversible conformational changes were observed upon FMN binding and release. The NMR structure of the FMN complex is in agreement with the crystal structure (PDB ID: 3EDO) and exhibits the characteristic flavodoxin fold, with a central five-stranded parallel β-sheet and five α-helices forming an α/β-sandwich architecture. The structure differs from other flavoproteins in that helix α2 is oriented perpendicular to the β-sheet and covers the FMN-binding site. This helix reversibly unfolds upon removal of the FMN ligand, which represents a unique structural rearrangement among flavodoxins.

A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [ 1 H, 1 H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

This study describes chirality- or template-mediated helical induction in achiral β-peptides for the first time. A strategy of end capping β-peptides derived from β-hGly (the smallest achiral β-amino acid) with a chiral β-amino acid that possesses a carbohydrate side chain (β-Caa; C-linked carbo β-amino acid) or a small, robust helical template derived from β-Caas, was adopted to investigate folding propensity. A single chiral (R)-β-Caa residue at the C- or N-terminus in these oligomers led to a preponderance of right-handed 12/10-helical folds, which was reiterated more strongly in peptides capped at both the C- and N-terminus. Likewise, the presence of a template (a 12/10-helical trimer) at both the C- and N-terminus resulted in a very robust helix. The propagation of the helical fold and its sustenance was found in a homo-oligomeric sequence with as many as seven β-hGly residues. In both cases, the induction of helicity was stronger from the N terminus, whereas an anchor at the C terminus resulted in reduced helical propensity. Although these oligomers have been theoretically predicted to favor a 12/10-mixed helix in apolar solvents, this study provides the first experimental evidence for their existence. Diastereotopicity was found in both the methylene groups of the β-hGly moieties due to chirality. Additionally, the β-hGly units have shown split behavior in the conformational space to accommodate the 12/10-helix. Thus, end capping to assist chiralty- or template-mediated helical induction and stabilization in achiral β-peptides is a very attractive strategy.

Structural and electronic properties of diastereomers of tetrahydrofuran amino acids (TAA) derived tripeptide, Boc-TAA-Leu-Val-OMe, are studied using density functional theory. Predicted secondary folding patterns with hydrogen bonded pseudocycles of different sizes in peptides containing (2R,5S)-cis-TAA and (2S,5R)-cis-TAA are confirmed by detailed NMR studies of both, and single crystal X-ray analysis of the former. A novel unusual folding pattern emanating from three-centered hydrogen bond is found in peptide with (2R,5S)-cis relationship. Stereochemical control on the orientation of interacting sites is substantiated by structural analysis of the peptides. Using natural bonding orbital and atoms in molecules analyses, charge transfer interactions are analyzed. Copyright (C) 2010 John Wiley & Sons, Ltd.

A cyclic tetrapeptide is prepared from alternating (S)-beta-Caa (C-linked carbo-beta-amino acid) and (R)-Ama (alpha-aminoxy acid). Extensive NMR (in CDCl(3) solution) and mass spectral (MS) studies show its halide binding capacity, with a special affinity to the chloride ion. At higher concentration it was found to form molecular aggregates as evidenced from transmission electron microscopic and atomic force microscopic analysis, confirming the formation of nanorods.

Hybrid peptides are prepared from a C-linked carbo-beta-amino acid ester (R-beta-Caa) and an alpha-aminoxy acid (R-Ama) derived from S-lactic acid. Extensive NMR (in CDCl 3 solution), CD, and MD studies on the tetra- and hexapeptides led to identification of robust 12/10-mixed helices. The dipeptide repeat having an R-beta-Caa and an R-Ama thus provides a "new motif" to realize a 12/10-mixed helix, for the first time, in oligomers containing R-Ama. To understand the impact of side chains in the mixed helix formation, R-beta-Caa/Ama (with no substitution in Ama) and S-beta-hAla/R-Ama oligomers were investigated. NMR studies revealed the existence of 12/10-helices in these hybrid peptides, and the side chains of monomers were found to have a profound influence on their stabilities. These observations imply that the propensity of beta-amino acid to prefer a mixed 12/10-helix governs the structural behavior in these peptides. The structural consequences of the lone-pair repulsion between nitrogen and oxygen atoms result in a new and interesting structural motif which behaves like "pseudo" beta (3),beta(2)-peptides in generating 12/10-mixed helices.

An efficient and practical total synthesis of (+)-goniothalesdiol and its 2,5-epi analogue is described herein. The key features include a diastereoselective reduction of C-5 keto with Zn(BH4)(2) to generate the desired stereochemistry at C-5. The tetrahydrofuran backbone of natural goniothalesdiol was synthesized under basic conditions via epoxide formation, followed by in situ 5-exo opening of the epoxide ring with 7-benzoyloxy oxygen upon debenzoylation. For the 2,5-epi analogue, the tetrahydrofuran ring was formed via acid-catalyzed acetonide deprotection followed by concomitant S(N)2 displacement of the O-mesyl group at C-5 center with C-2-gamma-oxygen.

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A stereoselective synthesis of the ABCD ring framework of azaspiracid-1 and azaspiracid-3 has been achieved using a tandem bis-spiroketalization protocol in the presence of a mild proton source from 1,4-diketone precursor. A tetrahydrofuran intermediate with the correct stereochemistry for the D ring of azaspiracids-1 and 3 was then taken through a linear sequence of reactions to afford the desired diketone precursor. The D-ring of azaspiracid-1 was then constructed by employing a Sharpless asymmetric dihydroxylation followed by etherification using a homoallyl derivative. The structure of the ABCD ring framework with four contiguous rings was established by extensive NMR analysis.

A general strategy for the synthesis of deoxyazasugars from d-glucose is described. Ring-closing metathesis and stereoselective dihydroxylation reactions were used as key steps.

Syntheses of Boc-protected 4-amino- and 5-amino-pyrrole-2-carboxylic acid methyl esters have been achieved and the structures of these compounds have been fully characterized by detailed NMR studies.

A novel, efficient synthesis of a series of functionalized, benzo-annelated decahydrofuro[3,2-h][1,6]naphthyridine derivatives 3 has been achieved. The protocol is based on the intramolecular hetero-Diels-Alder (IMHDA) reaction of in situ formed imines derived from an N-prenylated sugar aldehyde 1 and different aromatic amines 2 in the presence of bismuth(III) chloride as catalyst. The reactions could be run under very mild conditions at room temperature, and were complete within 30 min, affording exclusively and stereoselectively the corresponding trans-fused products 3 in good-to-excellent yields (Table).

Cyclic oligomers of tetrahydrofuran amino acids, cyclo( Taa1-Leu-Val)(2) ( left), cyclo-( Taa2-Leu-Val)(2) ( middle), and cyclo-( Taa2-Phe-Leu)(2) ( right), displayed well-defined intramolecularly hydrogen-bonded structures with distorted "beta-beta corner" motifs similar to the tennis ball seam.