Charged groups synergically enhance protein imprinting in amphoteric polyacrylamide cryogels

Proteins are amphoteric biopolymers with unevenly charged exterior surfaces. Taking this point fully into account could accomplish ingenious recognition systems for the biological macromolecues. Molecularly imprinted polymers (MIPs) are good tools to study the interactions between polymeric matrices and template molecules. Here different protein imprinted cryogels were prepared. Imprinting factors (IFs) were determined with bovine serum albumin (BSA) as the template. The IF of the polymeric cryogel made from only acrylamide (AM) and N,N′‐methylenebisacrylamide (BisAM) is about 1.38. The introduction of charged monomers, either acrylic acid or diallylamine, would increase IFs obviously. One of the basic cryogels gave the maximum IF (about 2.0) of that type. As both acrylic acid and diallylamine were involved, IFs were further increased. An amphoteric cryogel with a suitable acid‐base ratio gave a high IF of about 3.7. Whatever used alone or both, too many added acidic or basic monomers resulted in IF reduction. Taking full advantage of charged groups in MIPs could be a good way to manipulate protein–polymer interactions. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 133, 43851.     

Biomolecular Structure and Dynamics with Neutrons: The View from Simulation

The characterization of the structure and internal dynamics of biomolecules is essential to understanding their biological function. Neutron scattering probes similar time- and length-scales to molecular dynamics simulation. Hence, simulation models of biomolecules have become invaluable in the interpretation of experimental neutron data. Here, we report on advances in the application of simulation in developing neutron scattering to investigate internal protein motions and, as an example of industrial relevance, in the derivation of physical models of use in biofuel renewable energy research.     

Apparent heterogeneity of recombinant interferon γ receptors produced in prokaryotic and eukaryotic expression systems

Recombinant proteins show several types of heterogeneity and post-translational modifications which are usually related to their production system. The apparent heterogeneity of recombinant interferon γ receptors and interferon γ receptor–immunoglobulin G fusion proteins expressed in Escherichia coli, baculovirus-infected insect cells and Chinese hamster ovary cells have been studied. In general, all proteins tested showed some type of heterogeneity which was detectable by sodium dodecyl sulfate–polyacrylamide gel electrophoresis. The E. coli-derived receptor included non-native conformations involving mispaired or non-formed disulfides. This type of heterogeneity affected the biological activity of the protein. In addition, the prokaryotic protein had trapped phosphoric acid during downstream processing. The phosphoric acid entrapment did not affect ligand binding capacity. The eukaryotic proteins showed heterogeneity because of the unequal cleavage of the signal peptide and because of differences in glycosylation. The latter types of heterogeneity did not affect activity. Glycosylation-related heterogeneity was partially derived from the unequal utilization of the potential N-glycosylation sites and differently affected the apparent molecular masses and migrations of the proteins on polyacrylamide gels. The results may be useful in characterization studies of recombinant proteins.     

Apple Allergy: The cDNA Sequence of the Major Allergen of Apple,Determined by Performing PCR with a Primer Based on the N-Terminal Amino Acid Sequence,is Highly Homologous to the Sequence of the Major Birch Pollen Allergen

Considering the known N-terminal amino acid sequence of the major apple allergen, a polymerase chain reaction (PCR) primer was selected to amplify cDNA encoding this protein. A single PCR product was obtained, cloned into Escherichia coli and subsequently sequenced. The missing 5′-end of the apple cDNA sequence was obtained by a 5′-RACE method. The cDNA sequence showed 72% identity with the coding region of one of the known isoforms of Bet v 1, the major allergen of birch pollen. The deduced amino acid sequence resulted in a 158-residue protein with a calculated molecular mass of 17·5 kDa and 63% amino acid sequence identity to Bet v 1. In addition, further protein alignments showed a high degree of identity with allergens from other tree pollens and some ‘pathogenesis-related proteins’ from food plants. According to international regulations the allergen was termed Mal d 1 for this protein, it being the first major allergen discovered and characterised in fruits of apple (Malus domestica).     

SHM1: A multicopy suppressor of a temperature-sensitive null mutation in the HMG1-like abf2 gene

HM, an HMG1-like mitochondrial DNA-binding protein, is required for maintenance of the yeast mitochondrial genome when cells are grown in glucose. To better understand the role of HM in mitochondria, we have isolated several multicopy suppressors of the temperature-sensitive defect associated with an abf2 null mutation (lacking HM protein). One of these suppressors, SHM1, has been characterized at the molecular level and is described herein. SHM1 encodes a protein (SHM1p) that shares sequence similarity to a family of mitochondrial carrier proteins. On glycerol medium, where mitochondrial function is required for growth, shm1 deletion mutants are able to grow, whereas shm1 abf2 double mutants are severely inhibited. These results suggest that SHM1p plays an accessory role to HM in the mitochondrion. The GenBank Accession Number for the SHM1 sequence is U08352.     

Deciphering the Complex Molecular Pathogenesis of Myotonic Dystrophy Type 1 through Omics Studies

Omics studies are crucial to improve our understanding of myotonic dystrophy type 1 (DM1), the most common muscular dystrophy in adults. Employing tissue samples and cell lines derived from patients and animal models, omics approaches have revealed the myriad alterations in gene and microRNA expression, alternative splicing, 3′ polyadenylation, CpG methylation, and proteins levels, among others, that contribute to this complex multisystem disease. In addition, omics characterization of drug candidate treatment experiments provides crucial insight into the degree of therapeutic rescue and off-target effects that can be achieved. Finally, several innovative technologies such as single-cell sequencing and artificial intelligence will have a significant impact on future DM1 research.     

Secondary Structures of Proteins Follow Menzerath–Altmann Law

This article examines the presence of the empirical tendency known as the Menzerath–Altmann Law (MAL) on protein secondary structures. MAL is related to optimization principles observed in natural languages and in genetic information on chromosomes or protein domains. The presence of MAL is examined on a non-redundant dataset of 4728 proteins by verifying significant, negative correlations and testing classical and newly proposed formulas by fitting the observed trend. We conclude that the lengths of secondary structures are specifically dependent on their number inside the protein sequence, while possibly reflecting the formula proposed in this paper. This behavior is observed on average but is individually avoidable and possibly driven by a latent cost function. The data suggest that MAL could provide a useful guiding principle in protein design.