Influence Of Primary Structure Research Articles

Influence of Primary Structure on Fragmentation of Native-Like Proteins by Ultraviolet Photodissociation.

Analysis of native-like protein structures in the gas phase via native mass spectrometry and auxiliary techniques has become a powerful tool for structural biology applications. In combination with ultraviolet photodissociation (UVPD), native top-down mass spectrometry informs backbone flexibility, topology, hydrogen bonding networks, and conformational changes in protein structure. Although it is known that the primary structure affects dissociation of peptides and proteins in the gas phase, its effect on the types and locations of backbone cleavages promoted by UVPD and concomitant influence on structural characterization of native-like proteins is not well understood. Here, trends in the fragmentation of native-like proteins were evaluated by tracking the propensity of 10 fragment types (a, a+1, b, c, x, x+1, y, y-1, Y, and z) in relation to primary structure in a native-top down UVPD data set encompassing >9600 fragment ions. Differing fragmentation trends are reported for the production of distinct fragment types, attributed to a combination of both direct dissociation pathways from excited electronic states and those surmised to involve intramolecular vibrational energy redistribution after internal conversion. The latter pathways were systematically evaluated to evince the role of proton mobility in the generation of "CID-like" fragments through UVPD, providing pertinent insight into the characterization of native-like proteins. Fragmentation trends presented here are envisioned to enhance analysis of the protein higher-order structure or augment scoring algorithms in the high-throughput analysis of intact proteins.

Influence of Primary Structure on Responsiveness. Oxidative, Thermal, and Thermo-Oxidative Responses in Polysulfides

Using polymers with a double stimulus responsiveness, we show that primary structure, in addition to chemical composition, can significantly influence the response. This, however, applies to a stimulus of supramolecular nature (temperature) and not to a molecular one (oxidation). In the anionic ring-opening copolymerization of ethylene sulfide (ES) and propylene sulfide (PS), ES polymerizes faster and yields polysulfide chains with a gradient in composition; this primary structure can be varied by modifying the mode of monomer addition. Polysulfides with different primary structures (length of ES sequences) were linked to poly(ethylene glycol) (PEG) in amphiphilic block copolymers, whose (micellar) aggregates in water showed responsiveness to oxidants (solubilization) and gelation upon heating, similar to Pluronics. Both phenomena depended on composition (ES content), but only the second was affected by primary structure (the length of ES sequences), which was attributed to the influence of the latter on ...

Synthesis and Characterization of Sequence-Controlled Semicrystalline Comb Copolymers: Influence of Primary Structure on Materials Properties

Sequence-controlled semicrystalline copolymers were prepared by nitroxide-mediated copolymerization of a large excess of octadecylstyrene with small amounts of functional N-substituted maleimides (i.e., N-(n-propyl)maleimide, N-benzylmaleimide, pentafluorophenyl 4-maleimidobenzoate, 4-(N-maleimido)azobenzene, N-(1-pyrenyl)maleimide, and N-(2-(amino-BOC)ethylene)maleimide). These copolymers were prepared in bulk at 110 °C using the commercial alkoxyamine BlocBuilder MA as initiator and control agent. Time-controlled additions protocols were used to place the N-substituted maleimides at precise chain location along the poly(octadecylstyrene) backbones. Size exclusion chromatography and 1H NMR studies indicated that well-defined copolymers with controlled monomer sequences, composition, chain length, and molecular weight distribution were formed in all cases. Although possessing an atactic backbone, these polymers exhibit a semicrystalline behavior. The electron diffraction method indicated that the octadecy...

P96 Biostatistical/clinical issues in global drug development

Mutations in the influenza M2 membrane protein which confer resistance to the antiviral drug amantadine are exclusively located within the transmembrane region of the molecule. The influence of specific amino acid substitutions on the activity of the M2 protein in influenza A virus-infected cells is assessed in this report by their effects upon haemagglutinin (HA) stability and virus growth. A number of amino acid substitutions, e.g., L26H, A30T, S31 N and G34E reduced the activity of the M2 protein of A/chicken/Germany/34 (Rostock) and caused a substantial increase in expression of the low-pH form of HA. The adverse effects of the mutations on virus replication were evident from changes selected during subsequent passage of the mutant viruses in the presence or absence of amantadine: reversion to wt, the acquisition of a second suppressor mutation in M2, or the appearance of a complementary mutation in HA which increased its pH stability. In contrast, 127T and 127S, mutations which were most readily selected following passage of the wt virus in the presence of drug, caused an increase in M2 activity. Furthermore, in double mutants the 127T mutation suppressed the attenuating effects of the A30T and S31 N mutations on M2 activity. The influence of primary structure on the consequences of particular amino acid changes was further emphasized by the contrasting effects of the G34E mutation on the activities of two closely related proteins, causing an increase in the activity of the M2 of A/chicken/Germany/27 (Weybridge) as opposed to the decrease in activity of the Rostock protein. Estimates of differences in trans Golgi pH based on the degree of conversion of HA to the low-pH form, or complementation of differences in pH stability of mutant HAs, indicate that changes in M2 may influence pH within the transport pathway by as much as 0.6. The results thus provide further evidence that M2 regulates transmembrane pH gradients in the trans Golgi. Incompatibility between particular HA and M2 components and the selection of M2 mutants with suboptimal activity stresses the essential relationship between the structures and functions of these two virus proteins.

Influence of Primary Structure on Initial Free Radical Products Trapped in A:T Polydeoxynucleotides X-Irradiated at 4 K

EPR measurements were made at Q-band microwave frequencies on powder samples pressed into pellets and X-irradiated at 4 K. Measurements were made at 4 K after no anneal, then after a 77 K anneal, and then after a 300 K anneal. In poly(dA):poly(T) the free radical distribution is approximately a simple sum of the distributions in the separate homopolymers. In poly(dA-T) the free radical distribution differs from that of poly(dA):poly(T). The clearest difference is that in poly-(dA):poly(T) the concentration of one-electron-reduced thymine (Tre.) is reduced relative to the total radical concentration. On warming the thymine-containing samples from 77 K to room temperature, the Tox. radical disappears and the (T-H5'). radical appears. Also, the Tre. radical disappears and the (T + H6). radical appears. There are three main conclusions. First, little or no transfer of free radicals between strands is needed to explain the data. Second, when A and T are interstacked, either the Tre. radical is less stable against recombination than other radical products or radical transfer occurs to an adjacent adenine. Third, in the poly- and oligonucleotides, the Tox. radical is a likely precursor to the (T-H5'). radical.

Influence of amantadine resistance mutations on the pH regulatory function of the M2 protein of influenza A viruses

Mutations in the influenza M2 membrane protein which confer resistance to the antiviral drug amantadine are exclusively located within the transmembrane region of the molecule. The influence of specific amino acid substitutions on the activity of the M2 protein in influenza A virus-infected cells is assessed in this report by their effects upon haemagglutinin (HA) stability and virus growth. A number of amino acid substitutions, e.g., L26H, A30T, S31 N and G34E reduced the activity of the M2 protein of A/chicken/Germany/34 (Rostock) and caused a substantial increase in expression of the low-pH form of HA. The adverse effects of the mutations on virus replication were evident from changes selected during subsequent passage of the mutant viruses in the presence or absence of amantadine: reversion to wt, the acquisition of a second suppressor mutation in M2, or the appearance of a complementary mutation in HA which increased its pH stability. In contrast, 127T and 127S, mutations which were most readily selected following passage of the wt virus in the presence of drug, caused an increase in M2 activity. Furthermore, in double mutants the 127T mutation suppressed the attenuating effects of the A30T and S31 N mutations on M2 activity. The influence of primary structure on the consequences of particular amino acid changes was further emphasized by the contrasting effects of the G34E mutation on the activities of two closely related proteins, causing an increase in the activity of the M2 of A/chicken/Germany/27 (Weybridge) as opposed to the decrease in activity of the Rostock protein. Estimates of differences in trans Golgi pH based on the degree of conversion of HA to the low-pH form, or complementation of differences in pH stability of mutant HAs, indicate that changes in M2 may influence pH within the transport pathway by as much as 0.6. The results thus provide further evidence that M2 regulates transmembrane pH gradients in the trans Golgi. Incompatibility between particular HA and M2 components and the selection of M2 mutants with suboptimal activity stresses the essential relationship between the structures and functions of these two virus proteins.

Modeling of calcium-induced solubility profiles of casein for biotechnology: Influence of primary structure and posttranslational modification

Molecular biology holds the promise of new tools for the food industry which include proteins with tailor-made functionality. Without a fundamental knowledge of the molecular bases of these properties, implementation will be strictly empirical. For example, the phenomena of salt-induced precipitation of proteins (salting-out) and their resolubilization (salting-in) has heretofore been discussed only qualitatively. A quantitative method, using Wyman's theory of thermodynamic linkage, has been developed and tested on the calcium-induced solubility profiles of the major milk proteins, the caseins. Salting-out was described by a salt-binding constant,k1, andn, the number of moles of salt bound; salting-in was described by the corresponding termsk2 andm. The magnitude of these parameters indicated involvement of protein phosphate groups in binding and precipitation, but enzymatic dephosphorylation showed significant increases ink1 andk2 indicating involvement of carboxylate groups as well. Studies on two genetic variants of αs1-casein indicated the importance of a hydrophobically stabilized intramolecular ion pair in the functionality of the protein. These studies have led to a fuller understanding of the molecular basis for the solubility behavior of caseins and have laid the groundwork for future computer simulation of food protein functionality.