Similar Conformations Research Articles

The 2'-deoxyribofuranoside of 3-phenyltetrahydropyrimido[4,5-c]pyridazin-7-one: a bicyclic nucleoside with sugar residues in N and S conformations, and its molecular recognition.

The title compound 3-phenyltetrahydropyrimido[4,5-c]pyridazine 2'-deoxyribonucleoside [systematic name: 6-(2-deoxy-β-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-3-phenylpyrimido[4,5-c]pyridazin-7-one monohydrate, C17H18N4O4·H2O, 1] shows two conformations in the crystalline state and the two conformers (1a and 1b) adopt different sugar puckers. The sugar residue of 1a shows a C2'-endo S-type conformation, while 1b displays a C3'-endo N-type sugar pucker. Both conformers adopt similar anti conformations around the N-glycosylic bonds, with χ= -97.5 (3)° for conformer 1a and χ= -103.8 (3)° for conformer 1b. The extended crystalline network is stabilized by several intermolecular hydrogen bonds involving nucleoside and water molecules. The nucleobases and phenyl substituents of the two conformers (1a and 1b) are stacked and display a reverse alignment. A Hirshfeld surface analysis supports the hydrogen-bonding pattern, while curvedness surfaces visualize the stacking interactions of neighbouring molecules. The recognition face of nucleoside 1 for base-pair formation mimics that of 2'-deoxythymidine. Nucleoside 1 shows two pKa values: 1.8 for protonation and 11.2 for deprotonation. DNA oligonucleotides containing nucleoside 1 were synthesized and hybridized with complementary DNA strands. Nucleoside 1 forms a stable base pair with dA which is as stable as the canonical dA-dT pair. The bidentate 1-dA base pair is strengthened by a third hydrogen bond provided by the dA analogue 3-bromopyrazolo[3,4-d]pyrimidine-4,6-diamine 2'-deoxyribofuranoside (4). By this, duplex stability is increased and the suggested base-pairing patterns are supported.

NMR and vibrational spectroscopic studies on the structure and self-assembly of Two de novo dipeptides in methanol

Short peptides are known to form self-organized nano-architectures useful for advanced biomedical applications. Both hydrogen-bonding and hydrophobic interactions play a pivotal role in molecular assembly, including self-assembly of proteins and peptides. In the current investigation, we reported the synthesis, self-assembly pattern and physicochemical properties of two de novo dipeptides: N-Boc-(O-benzyl)-tyro-(dimethyl)-glutamate and N-Boc-(O-benzyl)-glu-(O-benzyl)-tyrosine-methyl ester, abbreviated as P1 and P2, respectively. These two peptides produced different morphological features under similar conditions due to the presence of a small twist in their molecular structures. In methanol, P1 gave rise to a unique fibrillar network whereas P2 self-assembled into oligomers of 20-30 nm diameters. The UV-Vis, FT-IR and Raman spectra were recorded using experimental methods and compared with the computational spectra obtained by density functional method (B3LYP/6-31G(d)). The electronic absorption spectra of both P1 and P2 measured in methanol showed broad absorption peaks in the UV region with an absorption maximum at ∼ 273 nm. FT-IR and Raman spectra of both the dipeptides in solid state showed amide I vibration bands at ∼1650 cm−1 indicating a similar conformation state of the peptide bonds. However, H/D exchange 1H NMR measurements confirmed that the amide NH of P1 was strongly involved in H-bond formation compared to P2 amide NH and rapid H/D exchange occurred upon addition of D2O in the solution. Thioflavin T (ThT) fluorescence assay measurement suggested that incubation of P1 in methanol at room temperature produced fibrillar aggregates enriched with compact ß-sheet conformation. Formation of such ordered structure also caused a blue shift in the amide-carbonyl Raman frequency of the peptide to ∼1657 cm−1. P1 fibrils further showed gel formation behaviour in 1:1 methanol/water mixture. The minimum gelation concentration (MGC) of the dipeptide was found to be 0.5% w/v and the calculated gelation temperature (Tgel) of the corresponding MGC was 67°C. On the other hand, the amide carbonyl stretching vibration of P2 appeared at ∼1650 cm−1 in the Raman spectra and it was not significantly altered in its oligomeric state (produced in methanol).Moreover, no significant enhancement of ThT fluorescence intensity of P2 indicating absence of compact ß-sheet conformation of the peptide. The P2 oligomers also showed no gel like phase transformation in methanol/water mixtures.

The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs.

It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks postzygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent postdivergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.

Using a fixed-jaw technique to achieve superior delivery accuracy and plan quality in single-isocenter multiple-target stereotactic radiosurgery for brain metastases

To quantify the influence of the minimum dynamic leaf gap (DLG) on delivery accuracy and plan quality and determine whether the fixed-jaw technique can be used to reduce the adverse effects of DLG in single-isocenter volumetric modulated arc therapy (VMAT) stereotactic radiosurgery (SRS) for multiple brain metastases (BMs). Twelve patients, each with two BMs, were enrolled in this study. For each patient, five simulated cases were generated by adjusting the intertarget distance (ITD; range, 1–5 cm). For each case, two single-isocenter VMAT SRS plans with and without the fixed-jaw technique were designed. For the plan without the fixed-jaw technique, the jaw positions were automatically set to cover two targets (AJ-VMAT). For the other plan, the jaw was fixed to cover one lesion when another lesion was irradiated (FJ-VMAT). Dosimetric parameters and delivery parameters of two plans were compared. FJ-VMAT plans achieved similar target conformity, lower dose spillages (V10%, V25%), and lower normal brain tissue (NBT) mean dose, and better gradient index than AJ-VMAT plans regardless of ITD but with more monitor units and longer beam-on time (P < 0.05). For ITD ≥2 cm, FJ-VMAT plans also yielded lower V50% and 12-Gy isodose volume for NBT compared to AJ-VMAT, and the reduction became more distinct as the ITD increased. In addition, FJ-VMAT generated a significantly higher gamma passing rate for each criterion (P < 0.05), especially for larger ITDs (≥2 cm) and tighter criteria (2%/1 mm) with a 4% improvement. Compared to conventional AJ-VMAT, FJ-VMAT could reduce the adverse effects from minimum DLG with superior delivery accuracy and plan quality in single-isocenter VMAT SRS for multiple BMs.

A C 54 B 2 Polycyclic π-System with Bilayer Assembly and Multi-Redox Activity

A C ₅₄ B ₂ Polycyclic π-System with Bilayer Assembly and Multi-Redox Activity

Phase transition and remodeling complex assembly are important for SS18-SSX oncogenic activity in synovial sarcomas

Oncoprotein SS18-SSX is a hallmark of synovial sarcomas. However, as a part of the SS18-SSX fusion protein, SS18’s function remains unclear. Here, we depict the structures of both human SS18/BRG1 and yeast SNF11/SNF2 subcomplexes. Both subcomplexes assemble into heterodimers that share a similar conformation, suggesting that SNF11 might be a homologue of SS18 in chromatin remodeling complexes. Importantly, our study shows that the self-association of the intrinsically disordered region, QPGY domain, leads to liquid-liquid phase separation (LLPS) of SS18 or SS18-SSX and the subsequent recruitment of BRG1 into phase-separated condensates. Moreover, our results show that the tyrosine residues in the QPGY domain play a decisive role in the LLPS of SS18 or SS18-SSX. Perturbations of either SS18-SSX LLPS or SS18-SSX’s binding to BRG1 impair NIH3T3 cell transformation by SS18-SSX. Our data demonstrate that both LLPS and assembling into chromatin remodelers contribute to the oncogenic activity of SS18-SSX in synovial sarcomas.

A bivalent Epstein-Barr virus vaccine induces neutralizing antibodies that block infection and confer immunity in humanized mice.

Epstein-Barr virus (EBV) is the major cause of infectious mononucleosis and is associated with several human cancers and, more recently, multiple sclerosis. Despite its prevalence and health impact, there are currently no vaccines or treatments. Four viral glycoproteins (gp), gp350 and gH/gL/gp42, mediate entry into the major sites of viral replication, B cells, and epithelial cells. Here, we designed a nanoparticle vaccine displaying these proteins and showed that it elicits potent neutralizing antibodies that protect against infection in vivo. We designed single-chain gH/gL and gH/gL/gp42 proteins that were each fused to bacterial ferritin to form a self-assembling nanoparticle. Structural analysis revealed that single-chain gH/gL and gH/gL/gp42 adopted a similar conformation to the wild-type proteins, and the protein spikes were observed by electron microscopy. Single-chain gH/gL or gH/gL/gp42 nanoparticle vaccines were constructed to ensure product homogeneity needed for clinical development. These vaccines elicited neutralizing antibodies in mice, ferrets, and nonhuman primates that inhibited EBV entry into both B cells and epithelial cells. When mixed with a previously reported gp350 nanoparticle vaccine, gp350D123, no immune competition was observed. To confirm its efficacy in vivo, humanized mice were challenged with EBV after passive transfer of IgG from mice vaccinated with control, gH/gL/gp42+gp350D123, or gH/gL+gp350D123 nanoparticles. Although all control animals were infected, only one mouse in each vaccine group that received immune IgG had detectable transient viremia. Furthermore, no EBV lymphomas were detected in immune animals. This bivalent EBV nanoparticle vaccine represents a promising candidate to prevent EBV infection and EBV-related malignancies in humans.

Structures of LIG1 engaging with mutagenic mismatches inserted by polβ in base excision repair

DNA ligase I (LIG1) catalyzes final ligation step following DNA polymerase (pol) β gap filling and an incorrect nucleotide insertion by polβ creates a nick repair intermediate with mismatched end at the downstream steps of base excision repair (BER) pathway. Yet, how LIG1 discriminates against the mutagenic 3′‐mismatches at atomic resolution remains undefined. Here, we determined X‐ray structures of LIG1/nick DNA complexes with G:T and A:C mismatches and uncovered the ligase strategies that favor or deter ligation of base substitution errors. Our structures revealed that LIG1 active site can accommodate G:T mismatch in a similar conformation with A:T base pairing, while it stays in the covalent LIG1‐adenylate intermediate during initial step of ligation reaction in the presence of A:C mismatch at 3′‐strand. Moreover, we showed mutagenic ligation and aberrant nick sealing of the nick DNA substrates with 3′‐preinserted dG:T and dA:C mismatches, respectively. Finally, we demonstrated that AP‐Endonuclease 1 (APE1), as a compensatory proofreading enzyme, interacts and coordinates with LIG1 during mismatch removal and DNA ligation. Our overall findings and ligase/nick DNA structures provide the features of accurate versus mutagenic outcomes at final BER steps where a multi‐protein complex including polβ, LIG1, and APE1 can maintain accurate repair.

4-[(Benzyl-amino)-carbon-yl]-1-methyl-pyridinium bromide hemihydrate: X-ray diffraction study and Hirshfeld surface analysis.

The hemihydrate of 4-[(benzyl-amino)-carbon-yl]-1-methyl-pyridinium bromide, C14H15N2O+·Br-·0.5H2O, was studied by single-crystal and powder X-ray diffraction methods. In the asymmetric unit, two organic cations of similar conformation, two bromide anions and one water mol-ecule are present. In the crystal, N-H⋯Br hydrogen bonds link the cations and anions. The formation of a set of inter-molecular C-H⋯Br and C-H⋯π inter-actions result in double chains extending parallel to [011]. A Hirshfeld surface analysis showed high contributions of H⋯H and C⋯H/H⋯C short contacts to the total Hirshfeld surfaces of the cations.

Clinical implementation of HyperArc.

The aim of this study was to present our experience on clinical implementation of HyperArc including dosimetric comparison between VMAT and HyperArc plans and dosimetric verification of HyperArc. In this study, eleven previously treated cases of brain metastasis were selected from our brain stereotactic radiotherapy program. The cases were retrospectively planned using HyperArc technique and the plan quality was evaluated. In addition, dosimetric effects of HyperArc plan with different energies and using jaw tracking technique were evaluated. Furthermore, dosimetric verification of HyperArc plans was performed using ion chamber and radiochromic film. Our results of dosimetric comparison shows that HyperArc technique improved both conformity index and gradient index compared to VMAT plans. We also found that using 6MV flattening filter free (6MV-FFF) beam improves gradient index in HyperArc plans compared to using 6MV flattening filter beam. Furthermore, our results show that jaw tracking technique reduces the size of low dose volume while maintaining similar target coverage, conformity index, and gradient index. In our dosimetric verification study, results of ion chamber and film measurement indicate no significant difference between VMAT and HyperArc plans. In conclusion, HyperArc simplifies planning of stereotactic treatment for brain and improves the dosimetry in treatment plans. Additionally, HyperArc provides for a safe and efficient treatment delivery system for stereotactic treatments to brain.

Biased agonists of the chemokine receptor CXCR3 differentially signal through Gαi:β-arrestin complexes.

G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and signal through the proximal effectors, G proteins and β-arrestins, to influence nearly every biological process. The G protein and β-arrestin signaling pathways have largely been considered separable; however, direct interactions between Gα proteins and β-arrestins have been described that appear to be part of a distinct GPCR signaling pathway. Within these complexes, Gαi/o, but not other Gα protein subtypes, directly interacts with β-arrestin, regardless of the canonical Gα protein that is coupled to the GPCR. Here, we report that the endogenous biased chemokine agonists of CXCR3 (CXCL9, CXCL10, and CXCL11), together with two small-molecule biased agonists, differentially formed Gαi:β-arrestin complexes. Formation of the Gαi:β-arrestin complexes did not correlate well with either G protein activation or β-arrestin recruitment. β-arrestin biosensors demonstrated that ligands that promoted Gαi:β-arrestin complex formation generated similar β-arrestin conformations. We also found that Gαi:β-arrestin complexes did not couple to the mitogen-activated protein kinase ERK, as is observed with other receptors such as the V2 vasopressin receptor, but did couple with the clathrin adaptor protein AP-2, which suggests context-dependent signaling by these complexes. These findings reinforce the notion that Gαi:β-arrestin complex formation is a distinct GPCR signaling pathway and enhance our understanding of the spectrum of biased agonism.

Investigation of liposomal self-adjuvanting peptide epitopes derived from conserved blood-stage Plasmodium antigens.

Malaria is a vector born parasitic disease causing millions of deaths every year. Despite the high mortality rate, an effective vaccine against this mosquito-borne infectious disease is yet to be developed. Up to date, RTS,S/AS01 is the only vaccine available for malaria prevention; however, its efficacy is low. Among a variety of malaria antigens, merozoite surface protein-1(MSP-1) and ring-infected erythrocyte surface antigen (RESA) have been proposed as promising candidates for malaria vaccine development. We developed peptide-based Plasmodium falciparum vaccine candidates that incorporated three previously reported conserved epitopes from MSP-1 and RESA into highly effective liposomal polyleucine delivery system. Indeed, MSP-1 and RESA-derived epitopes conjugated to polyleucine and formulated into liposomes induced higher epitope specific antibody titres. However, immunized mice failed to demonstrate protection in a rodent malaria challenge study with Plasmodium yoelii. In addition, we found that the three reported P. falciparum epitopes did not to share conformational properties and high sequence similarity with P. yoelii MSP-1 and RESA proteins, despite the epitopes were reported to protect mice against P. yoelii challenge.

The Structure of the Porcine Deltacoronavirus Main Protease Reveals a Conserved Target for the Design of Antivirals.

The existing zoonotic coronaviruses (CoVs) and viral genetic variants are important microbiological pathogens that cause severe disease in humans and animals. Currently, no effective broad-spectrum antiviral drugs against existing and emerging CoVs are available. The CoV main protease (Mpro) plays an essential role in viral replication, making it an ideal target for drug development. However, the structure of the Deltacoronavirus Mpro is still unavailable. Porcine deltacoronavirus (PDCoV) is a novel CoV that belongs to the genus Deltacoronavirus and causes atrophic enteritis, severe diarrhea, vomiting and dehydration in pigs. Here, we determined the structure of PDCoV Mpro complexed with a Michael acceptor inhibitor. Structural comparison showed that the backbone of PDCoV Mpro is similar to those of alpha-, beta- and gamma-CoV Mpros. The substrate-binding pocket of Mpro is well conserved in the subfamily Coronavirinae. In addition, we also observed that Mpros from the same genus adopted a similar conformation. Furthermore, the structure of PDCoV Mpro in complex with a Michael acceptor inhibitor revealed the mechanism of its inhibition of PDCoV Mpro. Our results provide a basis for the development of broad-spectrum antivirals against PDCoV and other CoVs.

Impact of distant peptide substrate residues on enzymatic activity of SlyD

Peptidyl-prolyl isomerases (PPIases) catalyze intrinsically slow and often rate-limiting isomerization of prolyl-peptide bonds in unfolded or partially folded proteins, thereby speeding up the folding process and preventing misfolding. They often possess binding and chaperone domains in addition to the domain carrying the isomerization activity. Although generally, their substrates display no identity in their amino acid sequence upstream and downstream of the proline with 20 possibilities for each residue, PPIases are efficient enzymes. SlyD is a highly efficient PPIase consisting of an isomerase domain and an additional chaperone domain. The binding of peptide substrates to SlyD and its enzymatic activity depend to some extend on the proline-proximal residues, however, the impact of proline-distant residues has not been investigated so far. Here, we introduce a label-free NMR-based method to measure SlyD activity on different peptide substrates and analysed the data in the context of obtained binding affinities and several co-crystal structures. We show that especially charged and aromatic residues up to eight positions downstream and three positions upstream of the proline and outside the canonical region of similar conformations affect the activity and binding, although they rarely display distinct conformations in our crystal structures. We hypothesize that these positions primarily influence the association reaction. In the absence of the chaperone domain the isomerase activity strongly correlates with substrate affinity, whereas additional factors play a role in its presence. The mutual orientation of isomerase and chaperone domains depends on the presence of substrates in both binding sites, implying allosteric regulation of enzymatic activity.

A Newly Synthesized β-amino-α, β-unsaturated Ketone Derivative of β-himachalene: Structural, NBO, NLO, and Molecular Docking Studies

In the current study, a new β-amino-α,β-unsaturated ketone-based himachalene ((1S,3R,8R)-9-amino-2,2-dichloro-3,7,7,10-tetramethyltricyclo[6.4.0.01,3]dodec-9-en-11-one) (4) was synthesized from β-himachalene (1) extracted from essential oil of Atlas Cedar. The β-amino-α, β-unsaturated ketone product (4) was characterized by 1D NMR (1H, 13C) and 2D NMR (HSQC, COSY, NOESY), FTIR analysis, and single-crystal X-ray diffraction. The title compound, C16H23Cl2NO, crystallizes with two molecules in the asymmetric unit with similar conformations. One of the two molecules is characterized by chlorine and one-methyl position disorder. In the crystal, intermolecular N—H…O hydrogen bonds lead to forming a three-dimensional framework. In addition, the molecular structure of the title compound was examined by Hirshfeld topology analysis and Density Functional Theory (DFT) using B3LYP calculations at 6-311+G(d,p) level. The optimized structure parameters were compared with the experimental result, an excellent correlation between theoretical structures parameters and experimental values was found. The natural bond orbitals (NBO) analysis and the first-order hyperpolarizability were also performed. Moreover, two biological activities were examined for product 4 against Acetylcholinesterase and Cytochrome P450 3A4, which bind to similar fragments with molecular docking. We find good scores and binding affinity of our molecule to link to these two proteins.

Identification of an Orally Bioavailable, Brain-Penetrant Compound with Selectivity for the Cannabinoid Type 2 Receptor.

Modulation of the endocannabinoid system (ECS) is of great interest for its therapeutic relevance in several pathophysiological processes. The CB2 subtype is largely localized to immune effectors, including microglia within the central nervous system, where it promotes anti-inflammation. Recently, a rational drug design toward precise modulation of the CB2 active site revealed the novelty of Pyrrolo[2,1-c][1,4]benzodiazepines tricyclic chemotype with a high conformational similarity in comparison to the existing leads. These compounds are structurally unique, confirming their chemotype novelty. In our continuing search for new chemotypes as selective CB2 regulatory molecules, following SAR approaches, a total of 17 selected (S,E)-11-[2-(arylmethylene)hydrazono]-PBD analogs were synthesized and tested for their ability to bind to the CB1 and CB2 receptor orthosteric sites. A competitive [3H]CP-55,940 binding screen revealed five compounds that exhibited >60% displacement at 10 μM concentration. Further concentration-response analysis revealed two compounds, 4k and 4q, as potent and selective CB2 ligands with sub-micromolar activities (Ki = 146 nM and 137 nM, respectively). In order to support the potential efficacy and safety of the analogs, the oral and intravenous pharmacokinetic properties of compound 4k were sought. Compound 4k was orally bioavailable, reaching maximum brain concentrations of 602 ± 162 ng/g (p.o.) with an elimination half-life of 22.9 ± 3.73 h. Whether administered via the oral or intravenous route, the elimination half-lives ranged between 9.3 and 16.7 h in the liver and kidneys. These compounds represent novel chemotypes, which can be further optimized for improved affinity and selectivity toward the CB2 receptor.

Crystal structure and Hirshfeld surface analysis of 3-methyl-4-oxo-N-phenyl-3,4-di-hydro-quinazoline-2-carbo-thio-amide.

The asymmetric unit of the title compound, C16H13N3OS, comprises two mol-ecules (A and B) with similar conformations that differ mainly in the orientation of the phenyl group relative to the rest of the mol-ecule, as expressed by the Cthio-amide-Nthio-amide-Cphen-yl-Cphen-yl torsion angle of 49.3 (3)° for mol-ecule A and of 5.4 (3)° for mol-ecule B. In the crystal, two inter-molecular N-H⋯N hydrogen bonds lead to the formation of a dimer with R 2 2(10) graph-set notation. A Hirshfeld surface analysis revealed that H⋯H inter-actions are the most important inter-molecular inter-actions, contributing 40.9% to the Hirshfeld surface.

Structural insights into apoptotic regulation of human Bfk as a novel Bcl-2 family member

Bcl-2 family kin (Bfk), also known as Bcl-2-like 15, plays an essential role in regulating apoptosis by eliciting weak pro-apoptotic responses in the gastrointestinal tract. Human Bfk is a novel Bcl-2 family protein owing to its unique domain composition involving BH2 and BH3. However, the molecular mechanism underlying the regulation of apoptosis by Bfk remains unclear. Here, we first report the crystal structure of human full-length Bfk. Surprisingly, the structure of Bfk adopts a canonical Bcl-2 fold but lacks the hydrophobic cleft, which could accommodate a BH3 domain from other Bcl-2 family proteins. Our biophysical interaction analysis proved that the full-length Bfk itself does not interact with multi-domain Bcl-2 family proteins or a BH3-containing peptide. Instead, Bfk is structurally and functionally reminiscent of Bid, a BH3-only protein in the Bcl-2 family, with similar conformations of helices α3-α5 and the specific motif in helix α5. Not only structural analyses of the full-length Bfk but also molecular dynamics simulation suggested that Bfk elicits its pro-apoptotic activity through a Bid-like apoptotic mechanism in which the BH3 domain is released upon caspase-mediated cleavage and a conformational change of the truncated form. Indeed, the BH3 peptide derived from Bfk exhibited in vitro interactions with Bcl-2, Bcl-XL, and Bak. These findings provide new insights into the molecular characteristics of Bfk and a valuable foundation for development of a new therapeutic target to control apoptosis.

Phosphorylation of the aggregate-forming protein alpha-synuclein on serine-129 inhibits its DNA-bending properties

Alpha-synuclein (aSyn) is a vertebrate protein, normally found within the presynaptic nerve terminal and nucleus, which is known to form somatic and neuritic aggregates in certain neurodegenerative diseases. Disease-associated aggregates of aSyn are heavily phosphorylated at serine-129 (pSyn), while normal aSyn protein is not. Within the nucleus, aSyn can directly bind DNA, but the mechanism of binding and the potential modulatory roles of phosphorylation are poorly understood. Here we demonstrate using a combination of electrophoretic mobility shift assay and atomic force microscopy approaches that both aSyn and pSyn can bind DNA within the major groove, in a DNA length-dependent manner and with little specificity for DNA sequence. Our data are consistent with a model in which multiple aSyn molecules bind a single 300 base pair (bp) DNA molecule in such a way that stabilizes the DNA in a bent conformation. We propose that serine-129 phosphorylation decreases the ability of aSyn to both bind and bend DNA, as aSyn binds 304 bp circular DNA forced into a bent shape, but pSyn does not. Two aSyn paralogs, beta- and gamma-synuclein, also interact with DNA differently than aSyn, and do not stabilize similar DNA conformations. Our work suggests that reductions in aSyn’s ability to bind and bend DNA induced by serine-129 phosphorylation may be important for modulating aSyn’s known roles in DNA metabolism, including the regulation of transcription and DNA repair.

Structural Characterization of the Human Cytosolic Malate Dehydrogenase I.

The first crystal structure of the human cytosolic malate dehydrogenase I (MDH1) is described. Structure determination at a high resolution (1.65 Å) followed production, isolation, and purification of human MDH1 using a bacterial expression system. The structure is a binary complex of MDH1 with only a bound malonate molecule in the substrate binding site. Comparisons of this structure with malate dehydrogenase enzymes from other species confirm that the human enzyme adopts similar secondary, tertiary, and quaternary structures and that the enzyme retains a similar conformation even when nicotinamide adenine dinucleotide (NAD+) is not bound. A comparison to the highly homologous porcine (sus scrofa) MDH1 ternary structures leads to the conclusion that only small conformational differences are needed to accommodate binding by NAD+ or other NAD+ mimetics. Conformational differences observed in the second subunit show that the NAD+ binding elements are nevertheless quite flexible. Comparison of hMDH1 to the human mitochondrial malate dehydrogenase (hMDH2) reveals some key differences in the α7−α8 loop, which lies directly beneath the substrate binding pocket. These differences might be exploited in the structure-assisted design of selective small molecule inhibitors of hMDH1, an emerging target for the development of anticancer therapeutics.