Residue-level interrogation of macromolecular crowding effects on protein stability

Theory predicts that macromolecular crowding affects protein behavior, but experimental confirmation is scant. Herein, we report the first residue-level interrogation of the effects of macromolecular crowding on protein stability. We observe up to a 100-fold increase in the stability, as measured by the equilibrium constant for folding, for the globular protein chymotrypsin inhibitor 2 (CI2) in concentrations of the cosolute poly(vinylpyrrolidone) (PVP) that mimic the protein concentration in cells. We show that the increased stability is caused by the polymeric nature of PVP and that the degree of stabilization depends on both the location of the individual residue in the protein structure and the PVP concentration. Our data reinforce the assertion that macromolecular crowding stabilizes the protein by destabilizing its unfolded states.     

Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction

Many unrelated proteins and peptides can assemble into amyloid or amyloid-like nanostructures, all of which share the cross-beta motif of repeat arrays of beta-strands hydrogen-bonded along the fibril axis. Yet, paradoxically, structurally polymorphic fibrils may derive from the same initial polypeptide sequence. Here, solid-state nuclear magnetic resonance (SSNMR) analysis of amyloid-like fibrils of the peptide hIAPP 20-29, corresponding to the region S (20)NNFGAILSS (29) of the human islet amyloid polypeptide amylin, reveals that the peptide assembles into two amyloid-like forms, (1) and (2), which have distinct structures at the molecular level. Rotational resonance SSNMR measurements of (13)C dipolar couplings between backbone F23 and I26 of hIAPP 20-29 fibrils are consistent with form (1) having parallel beta-strands and form (2) having antiparallel strands within the beta-sheet layers of the protofilament units. Seeding hIAPP 20-29 with structurally homogeneous fibrils from a 30-residue amylin fragment (hIAPP 8-37) produces morphologically homogeneous fibrils with similar NMR properties to form (1). A model for the architecture of the seeded fibrils is presented, based on the analysis of X-ray fiber diffraction data, combined with an extensive range of SSNMR constraints including chemical shifts, torsional angles, and interatomic distances. The model features a cross-beta spine comprising two beta-sheets with an interface defined by residues F23, A25, and L27, which form a hydrophobic zipper. We suggest that the energies of formation for fibril form containing antiparallel and parallel beta-strands are similar when both configurations can be stabilized by a core of hydrophobic contacts, which has implications for the relationship between amino acid sequence and amyloid polymorphism in general.     

Cinnamoyl Derivatives of 7α‐Amino‐ and 7α‐(Aminomethyl)‐ N‐(cyclopropylmethyl)‐6,14‐endo‐ethanotetrahydronororipavines are High‐Potency Opioid Antagonists

Methods have been developed for the synthesis of 7α‐amino‐ and 7α‐(aminomethyl)‐N‐cyclopropylmethyl‐6,14‐endo‐ethanotetrahydronororipavines and their cinnamoyl derivatives (Schemes 1 and 3). In displacement binding assays, the cinnamoyl derivatives 4c and 5c had high affinity for opioid receptors, but no particular selectivity for any receptor type or differences in affinity between 4c and 5c (Table 1). In tissue assays for opioid receptor function, in which both 4c and 5c were potent antagonists, the aminomethyl derivative 5c was 20‐ to 70‐fold more potent than the amino derivative 4c (Table 2). These data are in keeping with previously reported in vivo data and confirm the major effect of the methylene spacer in 5c .     

Stress relaxation in entangled melts of unlinked ring polymers

Stress relaxation in unlinked ring polymer melts poses an important challenge to our theoretical understanding of entangled polymer dynamics. Recent experiments on entangled unlinked ring melts show power-law stress relaxation with no hint of a rubbery plateau, usually the hallmark of entangled polymers. Here we present a theory for stress relaxation in rings analogous to the successful approach for star polymers. We augment our theory with mesoscale Monte Carlo dynamics simulations of equivalent "lattice animal" configurations. We find a stress relaxation function G(t)～t(-α) with α≈1/2 consistent with experiment, emerging ultimately from the disparate relaxation times of more- and less-central portions of ring conformations.     

Real time laser interference microscopy for bar‐spread polystyrene/poly(methyl methacrylate) blends

We demonstrate that real‐time laser interference microscopy can be used to directly observe the dynamics of film formation and phase separation processes for a bar‐spread polystyrene/poly(methyl methacrylate) blend. The ability to dynamically image laser interference patterns allows compete drying curves and polymer content to be determined throughout the film formation process. The polymer content at which phase separation structure first is observed in the interference micrograph sequence is in good agreement with calculated spinodal curves. Morphology evolution proceeds from phase separation onward via coarsening and coalescence to arrive at the final domain structure. In comparison, spin coating the same polymer blend results in structure evolution being quenched further from equilibrium due to the faster drying rate. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 985–992     

Sample preparation strategies for high‐throughput mass spectrometry imaging of primary tumor organoids

Patient‐derived 3D organoids show great promise for understanding patient heterogeneity and chemotherapy response in human‐derived tissue. The combination of organoid culture techniques with mass spectrometry imaging provides a label‐free methodology for characterizing drug penetration, patient‐specific response, and drug biotransformation. However, current methods used to grow tumor organoids employ extracellular matrices that can produce small molecule background signal during mass spectrometry imaging analysis. Here, we develop a method to isolate 3D human tumor organoids out of a Matrigel extracellular matrix into gelatin mass spectrometry compatible microarrays for high‐throughput mass spectrometry imaging analysis. The alignment of multiple organoids in the same z‐axis is essential for sectioning organoids together and for maintaining reproducible sample preparation on a single glass slide for up to hundreds of organoids. This method successfully removes organoids from extracellular matrix interference and provides an organized array for high‐throughput imaging analysis to easily identify organoids by eye for area selection and further analysis. With this method, mass spectrometry imaging can be readily applied to organoid systems for preclinical drug development and personalized medicine research initiatives.     

Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis

A-tracts are sequences of repeated adenine bases that, under the proper conditions, are capable of mediating DNA curvature. A-tracts occur naturally in the regulatory regions of many organisms, yet their biological functions are not fully understood. Orienting multiple A-tracts together constructively or destructively in a phase has the potential to create different shapes in the DNA helix axis. One means of detecting these molecular shape differences is from altered DNA mobilities measured using electrophoresis. The small molecule netropsin binds the minor groove of DNA, particularly at AT-rich sequences including A-tracts. Here, we systematically test the hypothesis that netropsin binding eliminates the curvature of A-tracts by measuring the electrophoretic mobilities of seven 98-base pair DNA samples containing different numbers and arrangements of centrally located A-tracts under varying conditions with netropsin. We find that netropsin binding eliminates the mobility difference between the DNA fragments with different A-tract arrangements in a concentration-dependent manner. This work provides evidence for the straightening of A-tracts upon netropsin binding and illustrates an artificial approach to re-sculpt DNA shape.