Small molecule recognition of c-Src via the Imatinib-binding conformation

The cancer drug, Imatinib, is a selective Abl kinase inhibitor that does not inhibit the closely related kinase c-Src. This one drug and its ability to selectively inhibit Abl over c-Src has been a guiding principle in virtually all kinase drug discovery efforts in the last 15 years. A prominent hypothesis explaining the selectivity of Imatinib is that Abl has an intrinsic ability to adopt an inactive conformation (termed DFG-out), whereas c-Src appears to pay a high intrinsic energetic penalty for adopting this conformation, effectively excluding Imatinib from its ATP pocket. This explanation of the difference in binding affinity of Imatinib for Abl versus c-Src makes the striking prediction that it would not be possible to design an inhibitor that binds to the DFG-out conformation of c-Src with high affinity. We report the discovery of a series of such inhibitors. We use structure-activity relationships and X-ray crystallography to confirm our findings. These studies suggest that small molecules are capable of inducing the generally unfavorable DFG-out conformation in c-Src. Structural comparison between c-Src in complex with these inhibitors allows us to speculate on the differential selectivity of Imatinib for c-Src and Abl.     

Electron spin resonance analysis of paramagnetic Pd(I) species in Pd(II)-exchanged H-rho zeolite

Zeolite rho was synthesized and Pd(II) exchanged into it. Pd(II) was reduced to paramagnetic Pd(1) by a thermal activation process. The interactions of Pd(I) in zeolite H-rho with oxygen, water, methanol, ammonia, carbon monoxide and ethylene have been studied by electron spin resonance (ESR) and electron spin echo modulation (ESEM) spectroscopies. The ESR spectrum of an activated sample shows the formation of one Pd(I) species. Pd(I) interacts with water vapor or molecular oxygen to form Pd(II)–O₂, indicating decomposition of water. Equilibration with methanol results in a broad isotropic ESR signal which is attributed to the formation of small palladium clusters. ESEM shows that the Pd clusters coordinate one molecule of methanol. Adsorption of ammonia produces a Pd(I) complex containing four molecules of ammonia based upon resolved nitrogen superhyperfine coupling. Adsorption of carbon monoxide results in a Pd(I) complex containing two molecules of carbon monoxide based upon resolved¹³C superhyperfine coupling. ESR and ESEM results indicate that exposure to ethylene leads to two new Pd(I) species each of which coordinates one molecule of ethylene.     

Prototyping an ionization source for non-engineers

Novel mass spectrometry (MS) based analytical platforms have enabled scientists to detect and quantify molecules within biological and environmental samples more accurately. Novel MS instrumentation starts as a prototype and, after years of development, can become a commercial product to be used by the larger MS community. Without the initial prototype, many MS-based instruments today would not be produced. Additionally, biotechnology companies are the main drivers for research, development, and production of novel instruments, but the tools for prototyping instrumentation have never been more accessible. Here, we present a tutorial on prototyping instrumentation through the case study of developing the Next Generation IR-MALDESI source to show that an engineering degree is not required to design and construct a prototype instrument with modern hardware and software. We discuss the prototyping process, the necessary skills required for efficient prototyping, and information about common hardware and software used within initial prototypes.     

Inhibitor scaffolds as new allele specific kinase substrates

The elucidation of protein kinase signaling networks is challenging due to the large size of the protein kinase superfamily (>500 human kinases). Here we describe a new class of orthogonal triphosphate substrate analogues for the direct labeling of analogue-specific kinase protein targets. These analogues were constructed as derivatives of the Src family kinase inhibitor PP1 and were designed based on the crystal structures of PP1 bound to HCK and N(6)-(benzyl)-ADP bound to c-Src (T338G). 3-Benzylpyrazolopyrimidine triphosphate (3-benzyl-PPTP) proved to be a substrate for a mutant of the MAP kinase p38 (p38-T106G/A157L/L167A). 3-Benzyl-PPTP was preferred by v-Src (T338G) (k(cat)/K(M) = 3.2 x 10(6) min(-)(1) M(-)(1)) over ATP or the previously described ATP analogue, N(6) (benzyl) ATP. For the kinase CDK2 (F80G)/cyclin E, 3-benzyl-PPTP demonstrated catalytic efficiency (k(cat)/K(M) = 2.6 x 10(4) min(-)(1) M(-)(1)) comparable to ATP (k(cat)/K(M) = 5.0 x 10(4) min(-)(1) M(-)(1)) largely due to a significantly better K(M) (6.4 microM vs 530 microM). In kinase protein substrate labeling experiments both 3-benzyl-PPTP and 3-phenyl-PPTP prove to be over 4 times more orthogonal than N(6)-(benzyl)-ATP with respect to the wild-type kinases found in murine spleenocyte cell lysates. These experiments also demonstrate that [gamma-(32)P]-3-benzyl-PPTP is an excellent phosphodonor for labeling the direct protein substrates of CDK2 (F80G)/E in murine spleenocyte cell lysates, even while competing with cellular levels (4 mM) of unlabeled ATP. The fact that this new more highly orthogonal nucleotide is accepted by three widely divergent kinases studied here suggests that it is likely to be generalizable across the entire kinase superfamily.     

Enhanced electron–phonon coupling at metal surfaces

Recent advances in experimental techniques and theoretical capabilities associated with the study of surfaces show promise for producing in unprecedented detail a picture of electron–phonon coupling. These investigations on surfaces of relatively simple metals can be the platform for understanding functionality in complex materials associated with the coupling between charge and the lattice. In this article, we present an introduction to electron–phonon coupling, especially in systems with reduced dimensionality, and the recent experimental and theoretical achievements. Then, we try to anticipate the exciting future created by advances in surface physics.     

Electronic interactions and phase transitions at surfaces and in low dimensions

Low-dimensional and magnetic systems provide particularly clear-cut cases for the study of modified electron states that result from coupling with elementary excitations. Electronic quasiparticles of enhanced mass have been observed on the energy scale of phonons, and very recently on that of spin waves. Such mechanisms have bearing for superconducting pair formation, as spin fluctuations are being considered for high-temperature superconductivity. Phase transitions can occur if these interactions are accompanied by a nesting condition in the Fermi surface, leading to charge- or spin-density waves. The phase transition usually involves a structural distortion and is characterized by the opening of an energy gap. Special cases are the presence of multiple bands at the Fermi surface or the occurrence of thermal fluctuations. Recent progress in photoelectron spectroscopy and synchrotron-radiation instrumentation allow us to study these effects directly and resolved in k-space. Observations on surfaces, in magnetic materials, and in quasi-one-dimensional crystals are presented. PACS 73.20.At; 71.38.-k; 75.30.Ds; 71.30.+h; 79.60.-i     

Single molecule studies of quantum dot conjugates in a submicrometer fluidic channel

A microfluidic and optical system was created for the detection and analysis of single molecules in solution. Fluidic channels with submicrometer dimensions were used to isolate, detect and identify individual quantum dots conjugated with organic fluorophores. The channels were fabricated in fused silica with a 500 nm square cross section. The resulting focal volume of approximately 500 aL reduced fluorescent background and increased the signal to noise ratio of single molecule detection. The channels also enabled the rapid detection of 99% of quantum dots and organic fluorophores traversing the focal volume. Conjugates were driven through the channels electrokinetically at 2.3 kV cm(-1), excited with a single 476 nm wavelength laser and detected with a confocal microscope. Fluorescence emission was collected simultaneously from green (500-590 nm) and red (610-680 nm) regions of the spectrum. Signal rejection was minimized by the narrow and symmetric emission spectra of the quantum dots. To demonstrate efficient multicolor detection and characterization of single molecule binding, Qdot 655 Streptavidin Conjugates were bound to Alexa Fluor 488 molecules and individually detected. Photon counting histogram analysis was used to quantify coincident detection and degree of binding. Fluorescence correlation spectroscopy was used to measure the mobility of bound and unbound species. The union of fluidic channels with submicrometer dimensions and quantum dots as fluorescent labels resulted in efficient and rapid multiplexed single molecule detection and analysis.