Structure Determination Research Articles

DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories.

This work describes a fast implementation of a software algorithm associated with determination of protein secondary structure based on the Define Secondary Structure of Proteins (DSSP) algorithm. This implementation is fully compatible with the DSSP v.4 and DSSP v.2 algorithms and implemented as a native GROMACS trajectory analysis module, which allows us to analyze molecular dynamics trajectories without any restrictions of the original DSSP implementation. This implementation works much faster than the original DSSP v.4 and DSSP v.2 algorithms.

Spectroscopic Characterization of Hydrogen-Bonded 2,7-Diazaindole Water Complex Isolated in the Gas Phase.

We present a systematic experimental analysis of the 1:1 complex of 2,7-diazaindole (27DAI) with water in the gas phase. The complex was characterized by using two-color-resonant two-photon ionization (R2PI), laser-induced fluorescence (LIF), single vibronic level fluorescence (SVLF), and photoionization efficiency (PIE) spectroscopic methods. The 000 band of the S1←S0 electronic transition of the 27DAI-H2O complex was observed at 33,074 cm-1, largely red-shifted by 836 cm-1 compared to that of the bare 27DAI. From the R2PI spectrum, the detected modes at 141 (ν'Tx), 169 (ν'Ty), and 194 (ν'Ry) cm-1 were identified as the internal motions of the H2O molecule in the complex. However, these modes were detected at 115 (ν″Tx), 152 (ν″Ty), and 190 (ν″Ry) cm-1 in the ground state, which suggested a stronger hydrogen bonding interaction in the photo-excited state. The structural determination was aided by the detection of νNH and νOH values in the ground and excited state complexes using the FDIR and IDIR spectroscopies. The detection of νNH at 3414 and νOH at 3447 cm-1 in 27DAI-H2O has shown an excellent correlation with the most stable structure consisting of N(1)-H···O and OH···N(7) hydrogen-bonded bridging water molecule in the ground state. The structure of the complex in the electronic excited state (S1) was confirmed by the corresponding bands at 3210 (νNH) and 3265 cm-1 (νOH). The IR-UV hole-burning spectroscopy confirmed the presence of only one isomer in the molecular beam. The ionization energy (IE) of the 27DAI-H2O complex was obtained as 8.789 ± 0.002 eV, which was significantly higher than the 7AI-H2O complex. The higher IE values of N-rich molecules suggest a higher resistivity of such molecules against photodamage. The obtained structure of the 27DAI-H2O complex has explicitly shown the formation of a cyclic one-solvent bridge incorporating N(1)-H···O and O-H···N(7) hydrogen bonds upon microsolvation. The lower excitation and higher ionization energies of the 27DAI-H2O complex compared to 7AI-H2O established higher stabilization of N-rich molecules. The solvent clusters forming a linear bridge between the hydrogen/proton acceptor and donor sites in the complex can be considered as a stepping stone to investigate the photoinduced deactivation mechanisms in nitrogen containing biologically relevant molecules.

The structural basis for light harvesting in organisms producing phycobiliproteins.

Cyanobacteria, red algae, and cryptophytes produce two classes of proteins for light-harvesting: water-soluble phycobiliproteins and membrane-intrinsic proteins that bind chlorophylls and carotenoids. In cyanobacteria, red algae, and glaucophytes, phycobilisomes (PBS) are complexes of brightly colored phycobiliproteins and linker (assembly) proteins. To date, six structural classes of phycobilisomes have been described: hemiellipsoidal, block-shaped, hemidiscoidal, bundle-shaped, paddle-shaped, and far-red-light bicylindrical. Two additional antenna complexes containing single types of phycobiliproteins have also been described. Since 2017, structures have been reported for examples of all of these complexes except bundle-shaped phycobilisomes by cryogenic electron microscopy. Phycobilisomes range in size from about 4.6 to 18 MDa and can include ∼900 polypeptides and bind >2000 chromophores. Cyanobacteria additionally produce membrane-associated proteins of the PsbC/CP43 superfamily of Chl a/b/d-binding proteins, including the iron-stress protein IsiA and other paralogous chlorophyll-binding proteins that can form antenna complexes with Photosystem I and/or Photosystem II. Red and cryptophyte algae also produce chlorophyll-binding proteins associated with Photosystem I but which belong to the chlorophyll a/b-binding (CAB) protein superfamily and which are unrelated to the chlorophyll-binding proteins (CBP) of cyanobacteria. This review describes recent progress in structure determination for phycobilisomes and the chlorophyll proteins of cyanobacteria, red algae, and cryptophytan algae.

Unusual Stabilisation of Remarkably Bent Tetra-Cationic Tetra-radical Intermolecular Fe(III) μ-Oxo Tetranuclear Complexes.

A hitherto unknown series of air stable, π-conjugated, remarkably bent tetra-cation tetra-radical intermolecular Fe(III) μ-oxo tetranuclear complex, isolated from the dication diradical diiron(III) porphyrin dimers, has been synthesised and spectroscopically characterised along with single crystal X-ray structure determination of two such molecules. These species facilitate long-range charge/radical delocalisation through the bridge across the entire tetranuclear unit manifesting an unusually intense NIR band. Assorted spin states of Fe(III) centres are stabilised within these unique tetranuclear frameworks: terminal six-coordinate iron centres stabilise the admixed intermediate spin states while the central five-coordinate iron centres stabilise the high-spin states. Variable temperature magnetic susceptibility measurements indicated strong antiferromagnetic coupling for the Fe(III)-O-Fe(III) unit while the exchange interactions between the Fe centres and the porphyrin π-cation radicals are weaker as supported both by magnetic data and DFT calculations. The nature of orbital overlap between the SOMOs of Fe(III) and π* orbital of the porphyrin was found to rationalise the observed exchange coupling, establishing such a complex magnetic exchange in this tetranuclear model with a significant bioinorganic relevance.

Diverse Reactivity of Amidinate-Supported Boron Centers with the Hypersilyl Anion and Access to a Monomeric Secondary Boron Hydride.

Diverse reactivity of the bulky tris(trimethylsilyl)silyl substituent [Si(SiMe3)3], also known as the hypersilyl group, was observed for amidinate-supported dichloro- and phenylchloroborane complexes. Treatment of the dichloroborane with potassium tris(trimethylsilyl)silyl led to the activation of the backbone β-carbon center and formation of saturated four-membered heterocyclic chloroboranes R'{Si(SiMe3)3}C(NR)2BCl [R' = Ph, R = Cy (3); R' = Ph, R = iPr (6); R' = tBu, R = Cy (8)], whereas the four-membered amidinate hypersilyl-substituted phenyl borane 4 {PhC(NCy)2B(Ph)[Si(SiMe3)3]} was observed for the case of an amidinate-supported phenylchloroborane. The highly deshielded 11B NMR spectroscopic resonance and the distinct difference in the 29Si NMR spectrum confirmed the presence of a σ-donating hypersilyl effect on compounds 3, 6, and 8. Reaction of 3 with the Lewis acid AlCl3 led to the formation of complex 11 in which an unusual cleavage of one of the C-N bonds of the amidinate backbone is observed. Nucleophilic substitution at the boron center of saturated chloroborane 3 with phenyllithium generated the phenylborane derivative 12, whereas the secondary monomeric boron hydride 13 was observed after treatment with alane (AlH3). All compounds (2-13) have been fully characterized by NMR spectroscopy and single-crystal X-ray structure determination studies.

Unusual Stabilisation of Remarkably Bent Tetra‐Cationic Tetra‐radical Intermolecular Fe(III) μ‐Oxo Tetranuclear Complexes

AbstractA hitherto unknown series of air stable, π‐conjugated, remarkably bent tetra‐cation tetra‐radical intermolecular Fe(III) μ‐oxo tetranuclear complex, isolated from the dication diradical diiron(III) porphyrin dimers, has been synthesised and spectroscopically characterised along with single crystal X‐ray structure determination of two such molecules. These species facilitate long‐range charge/radical delocalisation through the bridge across the entire tetranuclear unit manifesting an unusually intense NIR band. Assorted spin states of Fe(III) centres are stabilised within these unique tetranuclear frameworks: terminal six‐coordinate iron centres stabilise the admixed intermediate spin states while the central five‐coordinate iron centres stabilise the high‐spin states. Variable temperature magnetic susceptibility measurements indicated strong antiferromagnetic coupling for the Fe(III)−O−Fe(III) unit while the exchange interactions between the Fe centres and the porphyrin π‐cation radicals are weaker as supported both by magnetic data and DFT calculations. The nature of orbital overlap between the SOMOs of Fe(III) and π* orbital of the porphyrin was found to rationalise the observed exchange coupling, establishing such a complex magnetic exchange in this tetranuclear model with a significant bioinorganic relevance.

Prospective de novo drug design with deep interactome learning

De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. We present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of drug-like molecules. This method capitalizes on the unique strengths of both graph neural networks and chemical language models, offering an alternative to the need for application-specific reinforcement, transfer, or few-shot learning. It enables the “zero-shot" construction of compound libraries tailored to possess specific bioactivity, synthesizability, and structural novelty. In order to proactively evaluate the deep interactome learning framework for protein structure-based drug design, potential new ligands targeting the binding site of the human peroxisome proliferator-activated receptor (PPAR) subtype gamma are generated. The top-ranking designs are chemically synthesized and computationally, biophysically, and biochemically characterized. Potent PPAR partial agonists are identified, demonstrating favorable activity and the desired selectivity profiles for both nuclear receptors and off-target interactions. Crystal structure determination of the ligand-receptor complex confirms the anticipated binding mode. This successful outcome positively advocates interactome-based de novo design for application in bioorganic and medicinal chemistry, enabling the creation of innovative bioactive molecules.

Broadening environmental research in the era of accurate protein structure determination and predictions

Broadening environmental research in the era of accurate protein structure determination and predictions

Breaking Cycles: Saponification-Enhanced NMR Fingerprint Matching for the Identification and Stereochemical Evaluation of Cyclic Lipodepsipeptides from Natural Sources.

We previously described NMR based fingerprint matching with peptide backbone resonances as a fast and reliable structural dereplication approach for Pseudomonas cyclic lipodepsipeptides (CLiPs). In combination with total synthesis of a small library of configurational CLiP congeners this also allows unambiguous determination of stereochemistry, facilitating structure-activity relationship studies and enabling three-dimensional structure determination. However, the on-resin macrocycle formation in the synthetic workflow brings considerable burden and limits universal applicability. This drawback is here removed altogether by also transforming the native CLiP into a linearized analogue by controlled saponification of the ester bond. This eliminates the need for macrocycle formation, limiting the synthesis effort to linear peptide analogues. NMR fingerprints of such linear peptide analogues display a sufficiently distinctive chemical shift fingerprint to act as effective discriminators. The approach is developed using viscosin group CLiPs and subsequently demonstrated on putisolvin, leading to a structural revision, and tanniamide from Pseudomonas ekonensis COR58, a newly isolated lipododecapeptide that defines a new group characterized by a ten-residue large macrocycle, the largest to date in the Pseudomonas CLiP portfolio. These examples demonstrate the effectiveness of the saponification- enhanced approach that broadens applicability of NMR fingerprint matching for the determination of the stereochemistry of CLiPs.

The Phenix-AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix.

Advances in machine learning have enabled sufficiently accurate predictions of protein structure to be used in macromolecular structure determination with crystallography and cryo-electron microscopy data. The Phenix software suite has AlphaFold predictions integrated into an automated pipeline that can start with an amino acid sequence and data, and automatically perform model-building and refinement to return a protein model fitted into the data. Due to the steep technical requirements of running AlphaFold efficiently, we have implemented a Phenix-AlphaFold webservice that enables all Phenix users to run AlphaFold predictions remotely from the Phenix GUI starting with the official 1.21 release. This webservice will be improved based on how it is used by the research community and the future research directions for Phenix.

Determining Structures of Layer-by-Layer Spin-Coated Zinc Dicarboxylate-Based Metal-Organic Thin Films.

Thin films of crystalline solids with substantial free volume from organic chromophores and metal secondary building units (SBUs) are promising for engineering new optoelectronic properties through control of interchromophore coupling. Zn-based SBUs are especially relevant in this case because they avoid quenching the chromophore's luminescence. We find that layer-by-layer spin-coating using Zn acetate dihydrate and benzene-1,4-dicarboxylic acid (H2BDC) and biphenyl-4,4'-dicarboxylic acid (H2BPDC) linkers easily produces crystalline thin films. However, analysis of the grazing-incidence wide-angle X-ray scattering (GIWAXS) data reveals the structures of these films vary significantly with the linker, and metal-to-linker molar ratio used for fabrication. Under equimolar conditions, H2BPDC creates a type of structure like that proposed for SURMOF-2, whereas H2BDC generates a different metal-hydroxide-organic framework. Large excess of Zn2+ ions causes the growth of layered zinc hydroxides, irrespective of the linker used. Density functional theory (DFT) calculations provide structural models with minimum total energy that are consistent with the experimentally observed diffractograms. In the broader sense, this work illustrates the importance in this field of careful structural determination, e.g., by utilizing GIWAXS and DFT simulations to determine the structure of the obtained crystalline metal-organic thin films, so properties can be rationally engineered and explained.

Na3Ge2P3: A Zintl Phase Featuring [P3Ge-GeP3] Dimers as Building Blocks.

Recently, ternary lithium phosphidotetrelates have attracted interest particularly due to their high ionic conductivities, while corresponding sodium and heavier alkali metal compounds have been less investigated. Hence, we report the synthesis and characterization of the novel ternary sodium phosphidogermanate Na3Ge2P3, which is readily accessible via ball milling of the elements and subsequent annealing. According to single crystal X-ray structure determination, Na3Ge2P3 crystallizes in the monoclinic space group P21/c (no. 14.) with unit cell parameters of a = 7.2894(6) Å, b = 14.7725(8) Å, c = 7.0528(6) Å, β = 106.331(6)° and forms an unprecedented two-dimensional polyanionic network in the b/c plane of interconnected [P3Ge-GeP3] building units. The system can also be interpreted as differently sized ring structures that interconnect and form a two-dimensional network. A comparison with related ternary compounds from the corresponding phase system as well as with the binary compound GeP shows that the polyanionic network of Na3Ge2P3 resembles an intermediate step between highly condensed cages and discrete polyanions, which highlights the structural variety of phosphidogermanates. The structure is confirmed by 23Na- and 31P-MAS NMR measurements and Raman spectroscopy. Computational investigation of the electronic structure reveals that Na3Ge2P3 is an indirect band gap semiconductor with a band gap of 2.9 eV.

Structural characterization, thermal and morphological analysis of materialsat ecological park the Poma-Colombia

This place hosts rock shelters with cave paintings. The materials studied include: clays, substrates, and pigments in cave paintings. These materials were analyzed using various experimental techniques suitable for structure determination, thermal and morphological analysis. X-ray fluorescence energy dispersive (XRFED) was used to determine the basic composition. This is a versatile, fast, and non-destructive sampling technique used in the archaeological field because it uses a small sample and is not invasive. X-ray diffraction (XRD) is used to identify the clays and demonstrate the present phases. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) were used to observe the thermal behavior. These two techniques allow determining any event associated with a change in the thermal properties of a material with respect to temperature or time. Finally, in the morphological analysis, the study of grain size to the clay fraction was performed by scanning electron microscope (SEM).

Deciphering Local Structural Complexity in Zn/Ga-ZrO2 CO2 Hydrogenation Catalysts.

In the last few decades, massive effort has been expended in heterogeneous catalysis to develop new materials presenting high conversion, selectivity, and stability even under high-temperature and high-pressure conditions. In this context, CO2 hydrogenation is an interesting reaction where the catalyst local structure is strongly related to the development of an active and stable material under hydrothermal conditions at T/P > 300 °C/30 bar. In order to clarify the relationship between catalyst local ordering and its activity/stability, we herein report a combined laboratory and synchrotron investigation of aliovalent element (Ce/Zn/Ga)-containing ZrO2 matrixes. The results reveal the influence of similar average structures with different short-range orderings on the catalyst properties. Moreover, a further step toward the comprehension of the oxygen vacancy formation mechanism in Ce- and Ga-ZrO2 catalysts is reported. Finally, the reported results illustrate a robust method to guide local structure determination and ultimately help to avoid overuse of the "solid solution" definition.

Unlocking a new hydrogen-bonding marker: C-O bond shortening in vicinal diols revealed by rotational spectroscopy.

The conformational space of cis-1,2-cyclohexanediol, a model molecule for cyclic vicinal diols, was investigated using rotational spectroscopy and density functional theory calculations. Four low energy conformers within an energy window of 5 kJ mol-1 were identified computationally. A rotational spectrum of jet-cooled cis-1,2-cyclohexanediol was recorded with a chirped pulse Fourier transform microwave spectrometer. Two sets of rotational transitions were observed and could be assigned to conformers of cis-1,2-cyclohexanediol. The non-observation of other low energy conformers was explained by conformational conversion barrier height calculations and results from experimental spectra recorded with different carrier gases. Eight isotopologues, including those with 13C and 18O, of the lowest energy conformer were observed, allowing the determination of the semi-experimental equilibrium structure, reSE. Interestingly, the structural analysis revealed that the C-O bond length of the intramolecular hydrogen-bond donor is shorter than that of the acceptor. This appears to be a general characteristic of vicinal diols and can be used as a novel hydrogen-bond marker in such compounds.

Determination of Na+ Cation Locations in Nanozeolite ECR-1 Using a 3D ED Method

Until now, the comprehensive structural analysis of single crystals of zeolite ECR-1, an aluminosilicate with the EON topology, has been hindered owing to the submicron dimensions of the obtained crystals. Additionally, this zeolite, which is characterized by a topology comprising alternating periodic building units of MAZ and MOR layers, exhibits stacking faults that impede accurate refinement through the Rietveld method. In this report, we present, for the first time, the structure of ECR-1 elucidated by studying a nanocrystal with a significantly reduced number of stacking faults. The sample used was synthesized hydrothermally using trioxane as the organic structure-directing agent. The structure determination was conducted using precession electron diffraction (PED) at 103 K. Partial dehydration occurred owing to the high vacuum conditions in the TEM sample chamber. From the dynamical refinement (Robs = 0.097), 8.16 Na+ compensating cations were localized on six distinct crystallographic sites, along with approximately four water molecules per unit cell. Furthermore, a canonical Monte Carlo computational study was conducted to compare the experimental cationic distribution and location of water molecules with the simulation.

Template Synthesis of Disilacycloalkanes Utilizing the Reactivity of a Siloxane Bond.

The investigation of large and flexible macrocyclic compounds has garnered significant attention due to their functions as host molecules and linkers. Although the synthetic yields of such compounds, achieved by linking two molecular fragments, are often hindered by the flexibility of the molecular skeleton, one of the effective solutions is template synthesis for the macrocycles. In this study, a novel template synthesis for disilacycloalkanes by leveraging the reactivity of a siloxane bond was investigated. The yields obtained through the template methods surpassed those of the nontemplate approach, and the introduction of substituents to the silicon atoms was also accomplished with success. All of the resulting disilacycloalkanes crystallized exceptionally well, enabling their structural determination through X-ray crystallography. Notably, the stability of these structures was elucidated by analyzing dispersion forces between alkyl chains, using density functional theory (DFT) calculations. This template synthesis method demonstrates its efficacy in synthesizing molecular systems that encompass two functional moieties linked with macroalkanes.

Chiral Thianthrenes.

The absolute configuration and stability of two thianthrene chiral sulfoxides has been determined by means of X-ray single-crystal structure determinations. The analyses and configurations allow verification that the diastereomeric sulfoxides are stable in solution and are not interconverting, which has been suggested in some studies of sulfoxides. The two thianthrene sulfoxides have slightly different Rf values, which allowed their separation using flash chromatography on silica. The spots run back-to-back, which posed a challenge for their separation. The pure, separated compounds in solution remain as separate, single spots on a Thin Layer Chromatography (TLC) plate.

Synthesis of spiro-pyrrolizidine: Crystal structure and anticancer activity

A novel spiro-pyrrolizidine[2′-{[3,5-bis(benzyloxy)phenyl]carbonyl}-1′-(4-ethoxyphenyl)-1,1′,2,2′,5′,6′,7′7’a-octahydrospiro[indole-3,3′-pyrrolizine]-2-one (compound1) was synthesized via 1,3-dipolar cycloaddition of by refluxing 1-(3,5-bis(benzyloxy)phenyl)-3-(4-ethoxyphenyl)prop-2-en-1-one with isatin and L-proline. The structure was successfully elucidated by determination of single-crystal structures. The spiro-pyrrolizidine (1) crystallized in the triclinic centrosymmetric space group P1. The compound1 exhibits significant anticancer activity on MDA-MB 231 and HCT-116 cell lines with an IC50 values of 61.07± 0.98 µM and 62.5±70 µM respectively.

The role of good project governance in PPP project for toll road infrastructure in Indonesia

The use of infrastructure as a catalyst for Indonesia’s economic growth faces significant challenges. One example is the construction projects, which have not reached the intended goal and have led to an increase in investment cost compared to the original plan. Additionally, the interaction between the government and companies involved in toll-road construction projects under the public-private partnerships (PPP) mechanism has yet to produce good quality project governance and expected project performance. This study aimed to find empirical data on the determination of project intellectual capital and project ownership structure through good project governance on toll-road project performance in Indonesia. This study adopted a quantitative approach that involved data collected through a survey conducted among toll-road projects from 2015 to 2019. The data was analyzed with Structural Equation Modeling Partial Least Square (SEM-PLS). The results showed that project intellectual capital and project ownership structure significantly affected good project governance. Good project governance Practices significantly affected project performance. Project intellectual capital and project ownership structure influenced project performance through the mediation of good project governance. Conversely, two hypotheses were not supported by the data, i.e., the effect of project intellectual capital and project ownership structure on project performance. The findings of this research contributed to the literature regarding the implementation of collaborative governance in PPPs toll road development projects in Indonesia by providing a framework and assessment tools, which could be valuable for researchers and policymakers in analyzing and evaluating the governance and performance of toll road construction PPP projects.