The Effect of Biomarker Use on the Speed and Duration of Clinical Trials for Cancer Drugs.

Background: The purpose of this study was to explore the effects biomarkers have on the duration and speed of clinical trials in oncology.

Materials And Methods: Clinical trial data was pooled from www.clinicaltrials.

Rethinking enzyme kinetics: Designing and developing a biomolecular interactive tutorial (BIOMINT) learning tool for undergraduate students.

Enzyme kinetics is the study of enzymatic catalytic rates in biochemical reactions. This topic is commonly taught to life science students in introductory biochemistry courses during their undergraduate education. Unlike most other biochemistry topics, which focus on visual structures of biomolecules and their processes, enzyme kinetics is explained primarily through abstract mathematical and two-dimensional graphical plots.

Developing a three-dimensional animation for deeper molecular understanding of michaelis-menten enzyme kinetics.

The mathematical models that describe enzyme kinetics are invaluable predictive tools in numerous scientific fields. However, the daunting mathematical language used to describe kinetic behavior can be confusing for life science students; they often struggle to conceptualize and relate the mathematical representations to the molecular phenomena occurring at both macroscopic and microscopic levels. Students with less developed abstract and mathematical thinking skills may benefit from a visual learning approach.

Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases.

Helix-helix interactions: is the medium the message?

In this issue of Structure, Zhang and colleagues compare the helix-helix interaction spaces of an extensive database of soluble and membrane proteins. Intriguingly, the resultant clusters show similar helix interaction geometries between the protein classes, differing in detail only by patterns of local interactions and inter-helical distances.

Terminal residue hydrophobicity modulates transmembrane helix-helix interactions.

Central to the formation of tertiary structure in membrane protein folding is the presence of amino acid sequence motifs (such as "small-XXX-small" segments) in the TM segments that promote interaction-compatible surfaces through which the TM α-helices interact. Here, we sought to elucidate additional factors that may work in tandem to dictate the ultimate interaction fate of TM-embedded segments. In this context, we used proteolipid protein (PLP), the major protein from central nervous system myelin for which mutant-dependent non-native oligomerization has been implicated in neurological disorders, to explore the specific effects of TM boundary residues (the membrane entry and exit points), keying on the secondary structure and self-association of peptides corresponding to the PLP TM2 α-helix (wild-type sequence ⁶⁶AFQYVIYGTASFFFLYGALLLAEGF⁹⁰).

Membrane protein misassembly in disease.

Helix-helix interactions play a central role in the folding and assembly of integral α-helical membrane proteins and are fundamentally dictated by the amino acid sequence of the TM domain. It is not surprising then that missense mutations that target these residues are often linked to disease. In this review, we focus on the molecular mechanisms through which missense mutations lead to aberrant folding and/or assembly of these proteins, and then discuss pharmacological approaches that may potentially mitigate or reverse the negative effects of these mutations.

Novel hydrophobic standards for membrane protein molecular weight determinations via sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) is a universally employed technique that separates proteins on the basis of molecular weight (MW). However, membrane proteins are known to size anomalously on SDS-PAGE calibrated with conventional standards, an issue that complicates interpretation of protein identity, purity, degradation, and/or stoichiometry. Here we describe the preparation of novel polyleucine hydrophobic standards for SDS-PAGE that reduce the average deviation of the apparent MW from the formula MW of natural membrane proteins to 7% versus 20% with commercially available standards.

Modulation of the oligomerization of myelin proteolipid protein by transmembrane helix interaction motifs.

Proteolipid protein (PLP) is a highly hydrophobic 276-residue integral membrane protein that constitutes more than 50% of the total protein in central nervous system myelin. Previous studies have shown that this protein exists in myelin as an oligomer rather than as a monomer, and mutations in PLP that lead to neurological disorders such as Pelizaeus-Merzbacher disease and spastic paraplegia type 2 have been reported to affect its normal oligomerization. Here we employ peptide-based and in vivo approaches to examine the role of the TM domain in the formation of PLP quaternary structure through homo-oligomeric helix-helix interactions.

Deletion of a terminal residue disrupts oligomerization of a transmembrane alpha-helix.

In studies of the structural biology of membrane proteins, the success of strategies based on the "divide and conquer" approach, where peptides are used to model the individual transmembrane (TM) alpha-helices of membrane proteins, depends on the correct identification of the membrane-embedded TM alpha-helix amino acid sequence within the full-length protein. In the present work, we examine the effects of excluding or including TM boundary residues on the intrinsic properties of a Lys-tagged TM2 alpha-helix of myelin proteolipid protein (PLP), of parent sequence KKKK-66AFQYVIYGTASFFFLYGALLLAEG89-KKKK along with analogs containing an additional wild type Phe-90, Phe-90 and Tyr-91, and of a hydrophobic mutant Leu-90. Using protein gel electrophoresis, circular dichroism, and fluorescence resonance energy transfer in the membrane-mimetic detergent sodium dodecylsulfate (SDS), we demonstrate that the removal of a single amino acid from the C-terminus of this TM segment is enough to change its intrinsic properties, with TM2 66-89 displaying only a monomeric form, but with dimers arising for the other 3 peptides.

Characterization of an Escherichia coli sulfite oxidase homologue reveals the role of a conserved active site cysteine in assembly and function.

We report the biochemical and biophysical characterization of YedYZ, a sulfite oxidase homologue from Escherichia coli. YedY is a soluble catalytic subunit with a twin arginine leader sequence for export to the periplasm by the Tat translocation system. YedY is the only molybdoenzyme so far isolated from E.