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Self;#8208;Assembly of a 3D DNA Crystal Structure with Rationally Designed Six;#8208;Fold Symmetry
Abstract not provided
Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-Monophosphate
Cyclic nucleotide phosphodiesterases (PDEs) decompose second messengers cAMP and cGMP that play critical roles in many physiological processes. PDE1 of Saccharomyces cerevisiae has been subcloned and expressed in Escherichia coli . Recombinant yPDE1 has a K M of 110 μM and a k cat of 16.9 s⁻¹ for cAMP and a K M of 105 μM and a k cat of 11.8 s₅⁻¹ for cGMP. Thus, the specificity constant (k cat /K M cAMP )/(k cat /K M cGMP ) of 1.4 indicates a dual specificity of yPDE1 for hydrolysis of both cAMP and cGMP. The crystal structures of unliganded yPDE1 and its complex with GMP at 1.31 Å resolution reveal a new structural folding that is different from those of human PDEs but is partially similar to that of some other metalloenzymes such as metallo-β-lactamase. In spite of their different structures and divalent metals, yPDE1 and human PDEs may share a common mechanism for hydrolysis of cAMP and cGMP.
Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein
Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories in a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.
Probing Cytochrome c Folding Transitions upon Phototriggered Environmental Perturbations Using Time-Resolved X-ray Scattering
Direct tracking of protein structural dynamics during folding–unfolding processes is important for understanding the roles of hierarchic structural factors in the formation of functional proteins. As such, using cytochrome c (cyt c) as a platform, we investigated its structural dynamics during folding processes triggered by local environmental changes (i.e., pH or heme iron center oxidation/spin/ligation states) with time-resolved X-ray solution scattering measurements. Starting from partially unfolded cyt c, a sudden pH drop initiated by light excitation of a photoacid caused a structural contraction in microseconds, followed by active site restructuring and unfolding in milliseconds. In contrast, the reduction of iron in the heme via photoinduced electron transfer did not affect conformational stability at short timescales (<1 ms), despite active site coordination geometry changes. These results demonstrate how different environmental perturbations can change the nature of interaction between the active site and protein conformation, even within the same metalloprotein, which will subsequently affect the folding structural dynamics.
GL(3,C) invariance of type B 3-fold supersymmetric systems
Type B 3-fold supersymmetry is a necessary and sufficient condition for a quantum Hamiltonian to admit three linearly independent local solutions in closed form. We show that any such a system is invariant under GL(3,C) homogeneous linear transformations. In particular, we prove explicitly that the parameter space is transformed as an adjoint representation of it and that every coefficient of the characteristic polynomial appeared in 3-fold superalgebra is algebraic invariants. In the type A case, it includes as a subgroup the GL(2,C) projective transformation studied in the literature. We argue that any N-fold supersymmetric system has a GL(N,C) invariance for an arbitrary integral N.
Pattern formation on free surfaces via plastic buckling and periodic folding
Spontaneous formation of surface patterns such as folds and creases is widely observed in engineered systems, such as thin films and machined surfaces, as well as in natural systems such as floral petals and leaves. A recognized route for their formation is via surface elastic instabilities. Here we demonstrate an alternate route for their formation —plastic buckling and folding—that occurs when ductile materials are subject to large-strain (>1) deformation. Using in situ imaging of simple-shear deformation of polypropylene, we delineate the mechanics underlying formation of folds and the resulting surface morphology. Here, the fold pattern shows a single wavelength that scales linearly with the size of the plastic zone. An analytical model predicts onset of the plastic buckling instability and characteristics of the folds. Besides obvious applications for controllably generating surface features over large areas, our results suggest a contributing mechanism for origin of surface roughness in solids.
3-Fold and 6-Fold interpenetrating diamond nets based on the designed N,N'-dioxide 3,3'-benzo(c)cinnoline dicarboxylic acid with highly sensitive luminscence sensing for NACs and Fe{sup 3+} ion
Highlights: • The conjugated N,N'-dioxide 3,3'-benzo(c)cinnoline dicarboxylic acid was designed firstly here. • Two 3D diamond nets with 3-fold and 6-fold interpenetrating structures were constructed. • Compounds 1 and 2 exhibit highly luminescence quenching to Fe{sup III} ions and nitrobenzene derivatives. ABSTRACTBased on the designed conjugated ligand of N,N'-dioxide 3,3'-benzo(c)cinnoline dicarboxylic acid (H{sub 2}DBCD) with the aid of d{sup 10}-metal cations and two ancillary bis(imidazole) bridges, two 3D coordination polymers, namely, {[Cd(DBCD)(1,3-bib)]·(H_2O)_2}{sub n} (1), {[Zn(DBCD)(1,4-bib)]·(H_2O)_2}{sub n} (2), were constructed here. Structural analyses show compounds 1 and 2 are 3-fold and 6-fold interpenetrating dia nets, respectively. Further luminscence studies suggested that the two CPs can selectively and sensitively detect Fe{sup 3+} cation in aqueous solution and nitrobenzene derivatives nitrobenzene (NB), p-nitrotoluene (PNT), p-nitroaniline (PNA) and p-nitrophenol (PNP) in DMF.
Ring Separation Highlights the Protein-Folding Mechanism Used by the Phage EL-Encoded Chaperonin
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Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY
The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.
Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase
De novo macrocyclic peptides, derived using selection technologies such as phage and mRNA display, present unique and unexpected solutions to challenging biological problems. This is due in part to their unusual folds, which are able to present side chains in ways not available to canonical structures such as α-helices and β-sheets. Despite much recent interest in these molecules, their folding and binding behavior remains poorly characterized. In this work, we present cocrystallization, docking, and solution NMR structures of three de novo macrocyclic peptides that all bind as competitive inhibitors with single-digit nanomolar Ki to the active site of human pancreatic α-amylase. We show that a short stably folded motif in one of these is nucleated by internal hydrophobic interactions in an otherwise dynamic conformation in solution. Comparison of the solution structures with a target-bound structure from docking indicates that stabilization of the bound conformation is provided through interactions with the target protein after binding. These three structures also reveal a surprising functional convergence to present a motif of a single arginine sandwiched between two aromatic residues in the interactions of the peptide with the key catalytic residues of the enzyme, despite little to no other structural homology. Our results suggest that intramolecular hydrophobic interactions are important for priming binding of small macrocyclic peptides to their target and that high rigidity is not necessary for high affinity.
Observation of intercalation-driven zone folding in quasi-free-standing graphene energy bands
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Clustered BSRs: Evidence for gas hydrate-bearing turbidite complexes in folded regions, example from the Perdido Fold Belt, northern Gulf of Mexico
We detail previously undocumented but extensive gas hydrate accumulations in the mouth of Perdido Canyon in the northern Gulf of Mexico. The accumulations are located within central parts of structural domes (four-way closures) and are characterized by stacked, high-amplitude bottom simulating reflections (BSRs) that we call clustered BSRs. Seismic data from Perdido Canyon show two clustered BSRs associated with turbidite sequences within two dome folds formed from tectonic folding and salt diapir rise. The northwestern (NW) and southeastern (SE) clustered BSRs have aerial extents of ~25 km2 and 50 km2, respectively. Well log data confirm gas hydrate occurs above the NW clustered BSR, within a 225 m-thick consistently high-resistivity interval that we interpret as gas hydrate in near-vertical fractures and turbidite sands. The SE dome is only drilled at the edge of the BSR; nevertheless, the well log data indicate that a 30 m-thick gas hydrate accumulation is present. Gas chromatographic logs in both domes suggest a gradual transition from predominantly microbial gas below the BSR (500–1000 m below seafloor (mbsf)) to thermogenic gas at 1000–2000 mbsf. Based on the well log data and seismic stratigraphic analysis, we find gas hydrate is concentrated in fractures in marine mud, as well as in the pores of submarine fan turbidities, where saturations reach as high as 75%. An estimate of the total gas hydrate-bound gas volume at standard temperature and pressure is between 0.04 and 0.17 trillion cubic meters (TCM) assuming average hydrate saturation of 5-20% in a ~45 m thick turbidite sand unit above the Perdido Canyon BSR area. Measured BSR extent and gas volume estimates indicate that the NW and SE reservoirs are among the largest gas hydrate occurrences known in the Gulf of Mexico.
Quaternary structure independent folding of voltage-gated ion channel pore domain subunits
Every voltage-gated ion channel (VGIC) has a pore domain (PD) made from four subunits, each comprising an antiparallel transmembrane helix pair bridged by a loop. The extent to which PD subunit structure requires quaternary interactions is unclear. In this report we present crystal structures of a set of bacterial voltage-gated sodium channel (BacNa V ) 'pore only' proteins that reveal a surprising collection of non-canonical quaternary arrangements in which the PD tertiary structure is maintained. This context-independent structural robustness, supported by molecular dynamics simulations, indicates that VGIC-PD tertiary structure is independent of quaternary interactions. This fold occurs throughout the VGIC superfamily and in diverse transmembrane and soluble proteins. Strikingly, characterization of PD subunit-binding Fabs indicates that non-canonical quaternary PD conformations can occur in full-length VGICs. Together, our data demonstrate that the VGIC-PD is an autonomously folded unit. This property has implications for VGIC biogenesis, understanding functional states, de novo channel design, and VGIC structural origins.
Pressure induced polymerization of acetylide anions in CaC 2 and 10 7 fold enhancement of electrical conductivity
Pressure induced polymerization of CaC 2 in the amorphous phase is evidenced for the first time, accompanied by a 10 7 fold enhancement of the electrical conductivity.
A rare 4-fold interpenetrated metal–organic framework constructed from an anionic indium-based node and a cationic dicopper linker
We describe the synthesis and structure of a charged unique 4-fold interpenetrated MOF constructed from a new dicationic Robson-type dicarboxylate linker and a 4-connected In 3+ node.
Protein folds vs. protein folding: Differing questions, different challenges
We report protein fold prediction using deep-learning artificial intelligence (AI) has transformed the field of protein structure prediction. By combining physical and geometric constraints—and especially patterns extracted from the Protein Data Bank —these machine learning algorithms can predict protein structures at or near atomic resolution and do so in seconds. Today, these computational methods have now solved more than 200 million protein structures, which are accessible from the AlphaFold Protein Structure Database. This accomplishment seems all the more remarkable because few thought it possible or saw it coming. Deservedly, deep-learning AI was named Science magazine’s 2021 “breakthrough of the year”. Clearly, deep-learning AI represents a major advance in protein fold prediction.