Yunhuang Yang

Combining NMR and EPR Methods for Homodimer Protein Structure Determination

There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein complexes. One approach not yet widely used is to obtain intermediate and long-range distance constraints from paramagnetic relaxation enhancements (PRE) and electron paramagnetic resonance (EPR)-based techniques such as double electron electron resonance (DEER), which, when used together, can provide supplemental distance constraints spanning to 10-70 A. In this Communication, we describe integration of PRE and DEER data with conventional solution-state nuclear magnetic resonance (NMR) methods for structure determination of Dsy0195, a homodimer (62 amino acids per monomer) from Desulfitobacterium hafniense. Our results indicate that combination of conventional NMR restraints with only one or a few DEER distance constraints and a small number of PRE constraints is sufficient for the automatic NMR-based structure determination program CYANA to build a network of interchain nuclear Overhauser effect constraints that can be used to accurately define both the homodimer interface and the global homodimer structure. The use of DEER distances as a source of supplemental constraints as described here has virtually no upper molecular weight limit, and utilization of the PRE constraints is limited only by the ability to make accurate assignments of the protein amide proton and nitrogen chemical shifts.

Solution NMR structure of photosystem II reaction center protein Psb28 from Synechocystis sp. Strain PCC 6803

Oxygenic photosynthesis is initiated by photosystem II (PSII) in the thylakoid membranes of plants, algae and cyanobacteria. PSII is a multi-subunit pigment-protein complex responsible for splitting water into oxygen gas, hydrogen ions and electrons transferred to electron acceptors during photosynthesis.1 Two homologous membrane-spanning proteins D1 (PsbA) and D2 (PsbD) form the PSII complex core.1 Peripherally, two chlorophyll (Chl)-binding inner antenna proteins CP47 (PsbB) and CP43 (PsbC) are bound to the D1-D2 PSII complex core.1 These four large proteins are surrounded by a large number of smaller membrane proteins.2 Most of these small proteins have been observed in the crystal structures of the PSII complex from cyanobacteria.3,4 However, one small protein, Psb28, previously detected as a nonstoichiometric component of PSII,5 was not observed in the crystal structures indicating that Psb28 might not be a true PSII subunit. Recent studies revealed that Psb28 was preferentially bound to PSII core complex lacking CP43 (RC47) and involved in the biogenesis of CP47.6 Understanding the association of Psb28 with the PSII core complex should provide additional insight into its role in PSII-mediated function. However, the structure of Psb28 has remained unknown up until now. In this note, we report the solution NMR structure of Psb28 protein encoded by gene sll1398 [gi|952386] of Synechocystis sp. strain PCC 6803 (SWISS-PROT ID: PSB28_SYNY3, NESG target ID: SgR171).7 This protein, also named Psb13 or ycf79, belongs to the Psb28 protein family (Pfam ID: PF03912), which is currently made up of ~48 protein sequences (E score less than 0.001 using PSI-BLAST, Table S1). Both PSI-BLAST sequence similarity and Dali8 structure similarity searches indicate that this is the first atomic resolution structure available for the Psb28 family. ConSurf9 was used to identify conserved surface residues potentially involved in binding to the PSII core complex.10

Tumor-selective macromolecular MRI contrast agents

Tumor-selective macromolecular ligands containing 5-(p-Carbonyloxyphenyl)-10,15,20-triphenylporphyrin (HPTP) moiety (PHEA-DTPAHPTP and PAEA-DTPA-HPTP) were prepared by the incorporation of diethylenetriaminepentaacetic acid (DTPA) and 5-(p-hydroxylphenyl)-10,15, 20-triphenylporphyrin (HPTP) as the tumor-selective group in poly [α,β-(N-(2-hydroxyethyl)-L-aspartamide)] (PHEA) and poly-[α-β-(N-(2-aminoethy1)-L-aspartamide)] (PAEA). These ligands were further complexed with gadolinium chloride to form two tumor-selective macromolecular MRI contrast agents PHEA-Gd-DTPA-HPTP and PAEA-Gd-DTPA-HPTP. Relaxivity studies showed that both the polyaspartamide-gadolinium complexes possess higher relaxation effectiveness than that of the clinically used Gd-DTPA. Magnetic resonance imaging of tumors in mice indicated that these two polyaspartamide MRI contrast agents containing 5-(p-Carbonlyoxyphenyl)-10,15,20-triphenylporphyrin moiety can significantly enhance the contrast MRIs of Hepatoma (H22) and Ehrlich ascites carcinoma after injection and are taken up selectively by these cancers in mice.

Syntheses and reactivity of p-substituted benzonitrile complexes derived from dicyclopentadienyl-molybdenum and -tungsten. Oxidative electrochemistry. The crystal structure of [Mo(η5-C5H5)2(SC6H5)(p-(CH3)2NC6H4CN)][PF6]

Abstract New cationic complexes of the type [MCp 2 (SPh)( p -NCC 6 H 4 R)][PF 6 ] (M = Mo IV , W IV ; R = H, CH 3 , OCH 3 , NH 2 , N(CH 3 ) 2 , C 6 H 5 ) have been prepared by chemical oxidation of the parent bisthiolate in the presence of the corresponding benzonitrile derivative. Electrochemical studies, involving cyclic voltammetry carried out in dichloromethane and acetonitrile, showed a reversible or quasi-reversible oxidation for all the compounds. The molecular structure of [MoCp 2 (SPh)( p -NCC 6 H 4 N(CH 3 ) 2 )][PF 6 ] has been determined.

Structure-guided functional characterization of enediyne self-sacrifice resistance proteins, CalU16 and CalU19.

Calicheamicin γ1I (1) is an enediyne antitumor compound produced by Micromonospora echinospora spp. calichensis, and its biosynthetic gene cluster has been previously reported. Despite extensive analysis and biochemical study, several genes in the biosynthetic gene cluster of 1 remain functionally unassigned. Using a structural genomics approach and biochemical characterization, two proteins encoded by genes from the 1 biosynthetic gene cluster assigned as “unknowns”, CalU16 and CalU19, were characterized. Structure analysis revealed that they possess the STeroidogenic Acute Regulatory protein related lipid Transfer (START) domain known mainly to bind and transport lipids and previously identified as the structural signature of the enediyne self-resistance protein CalC. Subsequent study revealed calU16 and calU19 to confer resistance to 1, and reminiscent of the prototype CalC, both CalU16 and CalU19 were cleaved by 1in vitro. Through site-directed mutagenesis and mass spectrometry, we identified the site of cleavage in each protein and characterized their function in conferring resistance against 1. This report emphasizes the importance of structural genomics as a powerful tool for the functional annotation of unknown proteins.

A complete NMR spectral assignment of the lipid-free mouse apolipoprotein A-I (apoAI) C-terminal truncation mutant, apoAI(1-216).

ApoAI is the major protein component of the high-density lipoprotein (HDL) that has been a hot subject of interests because of its anti-atherogenic properties. Lipid-free apoAI specifically binds to phospholipids, triggering HDL formation. Here we report a complete backbone assignment and nearly complete sidechain assignment of a C-terminal 24-residue truncation mutant of mouse apoAI, apoAI(1-216), in its lipid-free form.

A community resource of experimental data for NMR / X‐ray crystal structure pairs

We have developed an online NMR / X‐ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X‐ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X‐ray crystallography. NMR spectroscopy and X‐ray diffraction data for 41 of these “NMR / X‐ray” structure pairs determined using conventional triple‐resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X‐ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl‐protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;69:449–465). These results demonstrate that the agreement between NMR and X‐ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR / X‐ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development.

Solution NMR structure of RHE_CH02687 from Rhizobium etli: A novel flavonoid‐binding protein

We report the solution NMR structure of RHE_CH02687 from Rhizobium etli. Its structure consists of two β‐sheets that together with two short and one long α‐helix form a hydrophobic cavity. This protein shows a high structural similarity to the prokaryotic protein YndB from Bacillus subtilis, and the eukaryotic protein Aha1. NMR titration experiments confirmed that RHE_CH02687, like its homolog YndB, interacted with flavonoids, giving support for a biological function as a flavonoid sensor in the symbiotic interaction between R. etli and plants. In addition, our study showed no evidence for a direct interaction between RHE_CH02687 and HtpG, the R. etli homolog of Hsp90. Proteins 2017; 85:951–956.

Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly

Protein domain family YabP (PF07873) is a family of small protein domains that are conserved in a wide range of bacteria and involved in spore coat assembly during the process of sporulation. The 62-residue fragment of Dsy0195 from Desulfitobacterium hafniense, which belongs to the YabP family, exists as a homodimer in solution under the conditions used for structure determination using NMR spectroscopy. The structure of the Dsy0195 homodimer contains two identical 62-residue monomeric subunits, each consisting of five anti-parallel beta strands (β1, 23–29; β2, 31–38; β3, 41–46; β4, 49–59; β5, 69–80). The tertiary structure of the Dsy0195 monomer adopts a cylindrical fold composed of two beta sheets. The two monomer subunits fold into a homodimer about a single C2 symmetry axis, with the interface composed of two anti-parallel beta strands, β1–β1′ and β5b–β5b′, where β5b refers to the C-terminal half of the bent β5 strand, without any domain swapping. Potential functional regions of the Dsy0195 structure were predicted based on conserved sequence analysis. The Dsy0195 structure reported here is the first representative structure from the YabP family.

Structural insights into the impact of two holoprosencephaly-related mutations on human TGIF1 homeodomain

Human protein TGIF1 is an essential regulator of cell fate with broad roles in different tissues, and has been implicated in holoprosencephaly (HPE) and many cancers. The function of TGIF1 in transcriptional regulation depends on its three-amino acid loop extension (TALE) type of homeodomain (HD). Two missense mutations that led to P192A and R219C substitutions in TGIF1-HD were previously found in HPE patients and suggested to be the causes for these cases. However, how these mutations affected TGIF1 function has not been investigated from a structural view. Here, we investigated the roles of P192 and R219 in TGIF1-HD structure packing through determining the NMR structure of TGIF1-HD. Surprisingly, P192 and R219 were found to play roles in packing α1 and α2 to α3 together with A190 and F215 through side-chain interactions. Circular dichroism (CD) showed that P192A and R219C mutants displayed structural change and less folding compared with wild-type TGIF1-HD, and 1H-15N HSQC spectrum of P192A mutant exhibited chemical shift perturbations in all three helices of TGIF1-HD. Thus, it is suggested that P192A and R219C mutations led to structure disturbances of TGIF1-HD, which subsequently reduced the DNA-binding affinity of TGIF1-HD by 23-fold and 10-fold respectively, as revealed by the isothermal titration calorimetry (ITC) experiments. Our study provides structural insights of the probable pathogenesis mechanism of two TGIF1-related HPE cases, and evidences for the roles of P192 and R219 in HD folding.