Time Window Expansion for HDX Analysis of an Intrinsically Disordered Protein

Application of typical HDX methods to examine intrinsically disordered proteins (IDP), proteins that are natively unstructured and highly dynamic at physiological pH, is limited because of the rapid exchange of unprotected amide hydrogens with solvent. The exchange rates of these fast exchanging amides are usually faster than the shortest time scale (10 s) employed in typical automated HDX-MS experiments. Considering the functional importance of IDPs and their association with many diseases, it is valuable to develop methods that allow the study of solution dynamics of these proteins as well as the ability to probe the interaction of IDPs with their wide range of binding partners. Here, we report the application of time window expansion to the millisecond range by altering the on-exchange pH of the HDX experiment to study a well-characterized IDP; the activation domain of the nuclear receptor coactivator, peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α). This method enabled mapping the regions of PGC-1α that are stabilized upon binding the ligand binding domain (LBD) of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ). We further demonstrate the method’s applicability to other binding partners of the IDP PGC-1α and pave the way for characterizing many other biologically important ID proteins.

Discovery of an NAD+ analogue with enhanced specificity for PARP1

Among various protein posttranslational modifiers, poly-ADP-ribose polymerase 1 (PARP1) is a key player for regulating numerous cellular processes and events through enzymatic attachments of target proteins with ADP-ribose units donated by nicotinamide adenine dinucleotide (NAD⁺). Human PARP1 is involved in the pathogenesis and progression of many diseases. PARP1 inhibitors have received approvals for cancer treatment. Despite these successes, our understanding about PARP1 remains limited, partially due to the presence of various ADP-ribosylation reactions catalyzed by other PARPs and their overlapped cellular functions. Here we report a synthetic NAD⁺ featuring an adenosyl 3′-azido substitution. Acting as an ADP-ribose donor with high activity and specificity for human PARP1, this compound enables labelling and profiling of possible protein substrates of endogenous PARP1. It provides a unique and valuable tool for studying PARP1 in biology and pathology and may shed light on the development of PARP isoform-specific modulators.

An analogue of nicotinamide adenine dinucleotide (NAD⁺) featuring an azido group at 3′-OH of adenosine moiety is found to possess high specificity for human PARP1-catalyzed protein poly-ADP-ribosylation.     

Variational principles and convergence of finite element approximations of a holonomic elastic-plastic problem

Summary It is shown that a boundary-value problem based on a holonomic elastic-plastic constitutive law may be formulated equivalently as a variational inequality of the second kind. A regularised form of the problem is analysed, and finite element approximations are considered. It is shown that solutions based on finite element approximation of the regularised problem converge.     

Photoinduced cycloadditions of electron deficient nitrones to alkenes

Oxaziridines are proposed as intermediates in the photoinduced cycloadditions of electron deficient nitrones to dipolarophiles.     

DNA sequencing

Determination of the sequence of DNA is one of the most important aspects of modern molecular biology. New sequencing methods currently being developed enable DNA sequence to be determined increasingly faster and more efficiently. One of the major advances in sequencing technology is the development of automated DNA sequencers. These utilize fluorescent rather than radioactive labels. A laser beam excites the fluorescent dyes, the emitted fluorescence is collected by detectors, and the information analyzed by computer. Robotic work stations are being developed to perform template preparation and purification, and the sequencing reactions themselves. Research is currently in progress to develop the technology of mass spectrometry for DNA sequencing. Success in this endeavor would mean that the gel electrophoresis step in DNA sequencing could be eliminated. A major innovation has been the application of polymerase chain reaction (PCR) technology to DNA sequence determination, which has led to the development of linear amplification sequencing (cycle sequencing). This very powerful yet technically simple method of sequencing has many advantages over conventional techniques, and may be used in manual or automated methods. Other recent innovations proposed recently to increase speed and efficiency include multiplex sequencing. This consists of pooling a number of samples and processing them as pools. After electrophoresis, the DNA is transferred to a membrane, and sequence images of the individual samples are obtained by sequential hybridizations with specific labeled oligonucleotides. Multiplex DNA sequencing has been used in conjunction with direct blotting electrophoresis to facilitate transfer of the DNA to a membrane. Chemiluminescent detection can also be used in conjunction with multiplex DNA sequencing to visualize the image on the membrane.     

Novel nonperipheral octa-3-hydroxypropylthio substituted metallo-phthalocyanines: synthesis,characterization, and investigation of their electrochemical,photochemical and computational properties

The current study describes the synthesis, electrochemical, computational, and photochemical properties of octa (3-hydroxypropylthio) substituted cobalt (II) ( 4 ), copper (II) ( 5 ), nickel (II) ( 6 ) and zinc(II) ( 7 ) phthalocyanine derivatives. These novel compounds were characterized by elemental analysis,¹H,¹³C NMR, FT-IR, UV-Vis, and MS. The redox behaviors of these metallo-phthalocyanines were investigated by the cyclic voltammetric method. The optimized molecular structure and gauge-including atomic orbital (GIAO)¹H and¹³C NMR chemical shift values of these phthalocyanines in the ground state had been calculated by using B3LYP/6–31G(d,p) basis set. The outcomes of the optimized molecular structure were given and compared with the experimental NMR values. The photochemical properties including photodegradation and singlet oxygen generation of zinc(II) phthalocyanine were studied in DMSO solution for the determination of its photosensitizer behaviors.     

Hydrogen bonding as the origin of both liquid crystallinity and polymer formation in some supramolecular materials

The use of lateral substitution on the aromatic rings of the diacid component of diacid/bispyridyl AABB supramolecular LC polymers is effective at retarding crystallization presumably by introducing a ‘carbuncle’ along the chain which interferes with the requisite efficient close packing of molecular units. We have examined both one and two chloro groups per ring and have observed a glass transition and fiber formation in the least crystalline complex.     

Fabrication and characterization of enhanced hydrazine electrochemical sensor based on gold nanoparticles decorated on the vanadium oxide,ruthenium oxide nanomaterials,and carbon nanotubes composites

This work describes the synthesis of mixed oxide film of vanadium and ruthenium by pulsed deposition technique on multiwall carbon nanotubes and the decoration of gold nanoparticles on the mixed film. A ternary electrocatalyst has been developed for the electrochemical oxidation of hydrazine by combining two metal oxide mixtures with Au nanoparticles. Surface morphology and chemical composition of the electrode have been examined with SEM, EDX, HRTEM, EIS, and XRD. The peak current of hydrazine increased 9 times at the AuNPs/(VOx-RuOx)/CNT/GCE compared to the bare GCE, and the peak potential shifted to negative 848 mV. Linear sweep voltammetry (LSV) and amperometric techniques revealed that the AuNPs/(VOx-RuOx)/CNT/GCE displays linear concentration range 2.5–10000 µM (LSV) and the concentration range 0.03–100 µM (amperometry). The limit of detection (LOD) is 0.5 μM and 0.1 μM at (S/N = 3) for LSV and amperometric technique, respectively. The results obtained show a good RSD% of 2.1%–3.2% and reasonable recovery of 97%–108% of hydrazine detection.