Determination of the orientation of an integral membrane protein and sites of glycosylation by oligonucleotide-directed mutagenesis: influenza B virus NB glycoprotein lacks a cleavable signal sequence and has an extracellular NH2-terminal region

NB protein does not affect influenza B virus replication in vitro and is not required for replication in or transmission between ferrets

The influenza B virus encodes a unique protein, NB, a membrane protein whose function in the replication cycle is not, as yet, understood. We engineered a recombinant influenza B virus lacking NB expression, with no concomitant difference in expression or activity of viral neuraminidase (NA) protein, an important caveat since NA is encoded on the same segment and initiated from a start codon just 4 nt downstream of NB. Replication of the virus lacking NB was not different to wild-type virus with full-length NB in clonal immortalized or complex primary cell cultures. In the mouse model, virus lacking NB induced slightly lower IFN-α levels in infected lungs, but this did not affect virus titres or weight loss. In ferrets infected with a mixture of viruses that did or did not express NB, there was no fitness advantage for the virus that retained NB. Moreover, virus lacking NB protein was transmitted following respiratory droplet exposure of sentinel animals. These data suggest no role for NB in supporting replication or transmission in vivo in this animal model. The role of NB and the nature of selection to retain it in all natural influenza B viruses remain unclear.

Palmitoylation is required for intracellular trafficking of influenza B virus NB protein and efficient influenza B virus growth in vitro

All influenza viruses bud and egress from lipid rafts within the apical plasma membrane of infected epithelial cells. As a result, all components of progeny virions must be transported to these lipid rafts for assembly and budding. Although the mechanism of transport for other influenza proteins has been elucidated, influenza B virus (IBV) glycoprotein NB subcellular localization and transport are not understood completely. To address the aforementioned properties of NB, a series of trafficking experiments were conducted. Here, we showed that NB co-localized with markers specific for the endoplasmic reticulum (ER) and Golgi region. The data from chemical treatment of NB-expressing cells by Brefeldin A, a fungal antibiotic and a known chemical inhibitor of the protein secretory pathway, further confirmed that NB is transported through the ER-Golgi pathway as it restricted NB localization to the perinuclear region. Using NB deletion mutants, the hydrophobic transmembrane domain was identified as being required for NB transport to the plasma membrane. Furthermore, palmitoylation was also required for transport of NB to the plasma membrane. Systematic mutation of cysteines to serines in NB demonstrated that cysteine 49, likely in a palmitoylated form, is also required for transport to the plasma membrane. Surprisingly, further analysis demonstrated that in vitro replication of NBC49S mutant virus was delayed relative to the parental IBV. The results demonstrated that NB is the third influenza virus protein to have been shown to be palmitoylated and together these findings may aid in future studies aimed at elucidating the function of NB.

Mapping the phosphoproteome of influenza A and B viruses by mass spectrometry

Protein phosphorylation is a common post-translational modification in eukaryotic cells and has a wide range of functional effects. Here, we used mass spectrometry to search for phosphorylated residues in all the proteins of influenza A and B viruses--to the best of our knowledge, the first time such a comprehensive approach has been applied to a virus. We identified 36 novel phosphorylation sites, as well as confirming 3 previously-identified sites. N-terminal processing and ubiquitination of viral proteins was also detected. Phosphorylation was detected in the polymerase proteins (PB2, PB1 and PA), glycoproteins (HA and NA), nucleoprotein (NP), matrix protein (M1), ion channel (M2), non-structural protein (NS1) and nuclear export protein (NEP). Many of the phosphorylation sites detected were conserved between influenza virus genera, indicating the fundamental importance of phosphorylation for all influenza viruses. Their structural context indicates roles for phosphorylation in regulating viral entry and exit (HA and NA); nuclear localisation (PB2, M1, NP, NS1 and, through NP and NEP, of the viral RNA genome); and protein multimerisation (NS1 dimers, M2 tetramers and NP oligomers). Using reverse genetics we show that for NP of influenza A viruses phosphorylation sites in the N-terminal NLS are important for viral growth, whereas mutating sites in the C-terminus has little or no effect. Mutating phosphorylation sites in the oligomerisation domains of NP inhibits viral growth and in some cases transcription and replication of the viral RNA genome. However, constitutive phosphorylation of these sites is not optimal. Taken together, the conservation, structural context and functional significance of phosphorylation sites implies a key role for phosphorylation in influenza biology. By identifying phosphorylation sites throughout the proteomes of influenza A and B viruses we provide a framework for further study of phosphorylation events in the viral life cycle and suggest a range of potential antiviral targets.

Structural and dynamic mechanisms for the function and inhibition of the M2 proton channel from influenza A virus

The M2 proton channel from influenza A virus, a prototype for a class of viral ion channels known as viroporins, conducts protons along a chain of water molecules and ionizable sidechains, including His37. Recent studies highlight a delicate interplay between protein folding, proton binding, and proton conduction through the channel. Drugs inhibit proton conduction by binding to an aqueous cavity adjacent to M2's proton-selective filter, thereby blocking access of proton to the filter, and altering the energetic landscape of the channel and the energetics of proton-binding to His37.

Molecular studies of influenza B virus in the reverse genetics era

Recovery of an infectious virus of defined genetic structure entirely from cDNA and the deduction of information about the virus resulting from phenotypic characterization of the mutant is the process of reverse genetics. This approach has been possible for a number of negative-strand RNA viruses since the recovery of rabies virus in 1994. However, the recovery of recombinant orthomyxoviruses posed a greater challenge due to the segmented nature of the genome. It was not until 1999 that such a system was reported for influenza A viruses, but since that time our knowledge of influenza A virus biology has grown dramatically. Annual influenza epidemics are caused not only by influenza A viruses but also by influenza B viruses. In 2002, two groups reported the successful recovery of influenza B virus entirely from cDNA. This has allowed greater depth of study into the biology of these viruses. This review will highlight the advances made in various areas of influenza B virus biology as a result of the development of reverse genetics techniques for these viruses, including (i) the importance of the non-coding regions of the influenza B virus genome; (ii) the generation of novel vaccine strains; (iii) studies into the mechanisms of drug resistance; (iv) the function(s) of viral proteins, both those analogous to influenza A virus proteins and those unique to influenza B viruses. The information generated by the application of influenza B virus reverse genetics systems will continue to contribute to our improved surveillance and control of human influenza.

Stability and function of the influenza A virus M2 ion channel protein is determined by both extracellular and cytoplasmic domains

A series of M2/NB chimeras were used to investigate the ion channel activity of the IAV M2 protein. Replacing the M2 cytoplasmic domain with the equivalent NB domain (AAB chimera) did not influence ion channel activity, while replacement of N-terminal domains (BAA and BAB chimeras) resulted in loss of activity. Extension of the M2 protein N-terminal domain resulted in full restoration of ion channel activity in BAA chimeras but only partial restoration in BAB. While not directly involved in ion channel activity, the N- and C-terminals of M2 are important for stabilization of the transmembrane domain structure.

Development of antivirals against influenza

Morbidity and mortality due to influenza virus infections remain a major problem throughout the world. Yearly, medical costs and loss of productivity resulting from influenza infection are estimated to be in the range of 12 dollars bn in the USA. The predicted increases in the elderly and immune-deficient populations will make influenza an even greater threat in the future. Despite the availability of vaccines, they have been least effective in these high-risk populations. Coupled with the requirement for routine revaccination, the need for effective antiviral agents is illustrated. The currently approved drugs, amantadine, rimantadine and ribavirin (in some countries), have limitations. They are only inhibitory against influenza A viruses, are prone to adverse reactions and quickly give rise to resistant virus. This review examines current drug therapies, antivirals in development and possible future opportunities for anti-influenza drugs.

Influenza B virus BM2 protein is an oligomeric integral membrane protein expressed at the cell surface

The influenza B virus BM2 protein contains 109 amino acid residues and it is translated from a bicistronic mRNA in an open reading frame that is +2 nucleotides with respect to the matrix (M1) protein. The amino acid sequence of BM2 contains a hydrophobic region (residues 7-25) that could act as a transmembrane (TM) anchor. Analysis of properties of the BM2 protein, including detergent solubility, insolubility in alkali pH 11, flotation in membrane fractions, and epitope-tagging immunocytochemistry, indicates BM2 protein is the fourth integral membrane protein encoded by influenza B virus in addition to hemagglutinin (HA), neuraminidase (NA), and the NB glycoprotein. Biochemical analysis indicates that the BM2 protein adopts an N(out)C(in) orientation in membranes and fluorescence microscopy indicates BM2 is expressed at the cell surface. As the BM2 protein possesses only a single hydrophobic domain and lacks a cleavable signal sequence, it is another example of a Type III integral membrane protein, in addition to M(2), NB, and CM2 proteins of influenza A, B, and C viruses, respectively. Chemical cross-linking studies indicate that the BM2 protein is oligomeric, most likely a tetramer. Comparison of the amino acid sequence of the TM domain of the BM2 protein with the sequence of the TM domain of the proton-selective ion channel M(2) protein of influenza A virus is intriguing as M(2) protein residues critical for ion selectivity/activation and channel gating (H(37) and W(41), respectively) are found at the same relative position and spacing in the BM2 protein (H(19) and W(23)).

Viral ion channels: structure and function

Viral ion channels are short auxiliary membrane proteins with a length of ca. 100 amino acids. They are found in enveloped viruses from influenza A, influenza B and influenza C (Orthomyxoviridae), and the human immunodeficiency virus type 1 (HIV-1, Retroviridae). The channels are called M2 (influenza A), NB (influenza B), CM2 (influenza C) and Vpu (HIV-1). Recently, in Paramecium bursaria chlorella virus (PBCV-1, Phycodnaviridae), a K+ selective ion channel has been discovered. The viral channels form homo oligomers to allow an ion flux and represent miniaturised systems. Proton conductivity of M2 is established; NB, Vpu and the potassium channel from PBC-1 conduct ions; for CM2 ion conductivity is still under proof. This review summarises the current knowledge of these short viral membrane proteins. Their discovery is outlined and experimental evidence for their structure and function is discussed. Studies using computational methods are presented as well as investigations of drug-protein interactions.

Viral ion channels: molecular modeling and simulation

In a number of membrane-bound viruses, ion channels are formed by integral membrane proteins. These channel proteins include M2 from influenza A, NB from influenza B, and, possibly, Vpu from HIV-1. M2 is important in facilitating uncoating of the influenza A viral genome and is the target of amantadine, an anti-influenza drug. The biological roles of NB and Vpu are less certain. In all cases, the protein contains a single transmembrane alpha-helix close to its N-terminus. Channels can be formed by homo-oligomerization of these proteins, yielding bundles of transmembrane helices that span the membrane and surround a central ion-permeable pore. Molecular modeling may be used to integrate and interpret available experimental data concerning the structure of such transmembrane pores. This has proved successful for the M2 channel domain, where two independently derived models are in agreement with one another, and with solid-state nuclear magnetic resonance (NMR) data. Simulations based on channel models may yield insights into possible ion conduction and selectivity mechanisms.

Co- and posttranslational translocation mechanisms direct cystic fibrosis transmembrane conductance regulator N terminus transmembrane assembly

Transmembrane topology of most eukaryotic polytopic proteins is established cotranslationally at the endoplasmic reticulum membrane through the action of alternating signal and stop transfer sequences. Here we demonstrate that the cystic fibrosis transmembrane conductance regulator (CFTR) achieves its N terminus topology through a variation of this mechanism that involves both co- and posttranslational translocation events. Using a series of defined chimeric and truncated proteins expressed in a reticulocyte lysate system, we have identified two topogenic determinants encoded within the first (TM1) and second (TM2) membrane-spanning segments of CFTR. Each sequence independently (i) directed endoplasmic reticulum targeting, (ii) translocated appropriate flanking residues, and (iii) achieved its proper membrane-spanning orientation. Signal sequence activity of TM1, however, was inefficient due to the presence of two charged residues, Glu92 and Lys95, located within its hydrophobic core. As a result, TM1 was able to direct correct topology for less than half of nascent CFTR chains. In contrast to TM1, TM2 signal sequence activity was both efficient and specific. Even in the absence of a functional TM1 signal sequence, TM2 was able to direct CFTR N terminus topology through a ribosome-dependent posttranslational mechanism. Mutating charged residues Glu92 and Lys95 to alanine improved TM1 signal sequence activity as well as the ability of TM1 to independently direct CFTR N terminus topology. Thus, a single functional signal sequence in either the first or second TM segment was sufficient for directing proper CFTR topology. These results identify two distinct and redundant translocation pathways for CFTR N terminus transmembrane assembly and support a model in which TM2 functions to ensure correct topology of CFTR chains that fail to translocate via TM1. This novel arrangement of topogenic information provides an alternative to conventional cotranslational pathways of polytopic protein biogenesis.

The CM2 protein of influenza C virus is an oligomeric integral membrane glycoprotein structurally analogous to influenza A virus M2 and influenza B virus NB proteins

We have undertaken a characterization of the CM2 protein of influenza C virus. The CM2 coding region of RNA segment 6 (nucleotides 731-1147) was cloned from two strains of influenza C virus and expressed using the vaccinia virus-bacteriophage T7 RNA polymerase (vac-T7) system. An antiserum raised to a C-terminal peptide in the CM2 open reading frame recognized the CM2 protein in influenza C virus-infected cells and after vac-T7 expression of the CM2 open reading frame. CM2 is posttranslationally modified by addition of high-mannose carbohydrate chains (Mr approximately 18 kDa) and by further addition of polylactosaminoglycans (Mr approximately 21-35 kDa). The available data indicate that CM2 has a cleavable signal peptide at the N-terminus of the protein. Site-directed mutagenesis eliminated the single potential N-linked carbohydrate attachment site on CM2 and indicated that the protein has an NoutCin orientation in membranes. Nonreducing SDS-PAGE indicated that the protein was expressed as disulfide-linked dimers and tetramers. Cell surface biotinylation and indirect immunofluorescence showed the protein to be expressed at the cell surface. Elimination of the N-linked carbohydrate attachment site and addition of a C-terminal HA epitope tag did not adversely affect surface expression of CM2. The NoutCin membrane orientation of CM2, the size of the ectodomain and cytoplasmic tail of CM2, and its ability to form disulfide-linked oligomers are reminiscent of the structural properties of influenza A virus M2 and influenza B virus NB proteins.

Membrane assembly of the triple-spanning coronavirus M protein. Individual transmembrane domains show preferred orientation

The M protein of mouse hepatitis virus strain A59 is a triple-spanning membrane protein which assembles with an uncleaved internal signal sequence, adopting an NexoCcyt orientation. To study the insertion mechanism of this protein, domains potentially involved in topogenesis were deleted and the effects analyzed in topogenesis were deleted and the effects analyzed in several ways. Mutant proteins were synthesized in a cell-free translation system in the presence of microsomal membranes, and their integration and topology were determined by alkaline extraction and by protease-protection experiments. By expression in COS-1 and Madin-Darby canine kidney-II cells, the topology of the mutant proteins was also analyzed in vivo. Glycosylation was used as a biochemical marker to assess the disposition of the NH2 terminus. An indirect immunofluorescence assay on semi-intact Madin-Darby canine kidney-II cells using domain-specific antibodies served to identify the cytoplasmically exposed domains. The results show that each membrane-spanning domain acts independently as an insertion and anchor signal and adopts an intrinsic preferred orientation in the lipid bilayer which corresponds to the disposition of the transmembrane domain in the wild-type assembled protein. These observations provide further insight into the mechanism of membrane integration of multispanning proteins. A model for the insertion of the coronavirus M protein is proposed.

Membrane assembly of the triple-spanning coronavirus M protein. Individual transmembrane domains show preferred orientation

The M protein of mouse hepatitis virus strain A59 is a triple-spanning membrane protein which assembles with an uncleaved internal signal sequence, adopting an NexoCcyt orientation. To study the insertion mechanism of this protein, domains potentially involved in topogenesis were deleted and the effects analyzed in topogenesis were deleted and the effects analyzed in several ways. Mutant proteins were synthesized in a cell-free translation system in the presence of microsomal membranes, and their integration and topology were determined by alkaline extraction and by protease-protection experiments. By expression in COS-1 and Madin-Darby canine kidney-II cells, the topology of the mutant proteins was also analyzed in vivo. Glycosylation was used as a biochemical marker to assess the disposition of the NH2 terminus. An indirect immunofluorescence assay on semi-intact Madin-Darby canine kidney-II cells using domain-specific antibodies served to identify the cytoplasmically exposed domains. The results show that each membrane-spanning domain acts independently as an insertion and anchor signal and adopts an intrinsic preferred orientation in the lipid bilayer which corresponds to the disposition of the transmembrane domain in the wild-type assembled protein. These observations provide further insight into the mechanism of membrane integration of multispanning proteins. A model for the insertion of the coronavirus M protein is proposed.

The transmembrane domain of influenza A M2 protein forms amantadine-sensitive proton channels in planar lipid bilayers

In a direct test of the hypothesis that the M2 coat protein of influenza A can function as a proton translocator, we incorporated a synthetic peptide containing its putative transmembrane domain into voltage-clamped planar lipid bilayers. We observed single proton-selective ion channels with a conductance of approximately 10 pS at a pH of 2.3, consistent with the association of several monomers around a central water-filled pore. The channels were reversibly blocked by the anti-influenza drug amantadine. These experiments imply a central role for M2 protein in virus replication and assembly and may explain the mechanism of action of amantadine. Analogous proteins may have a similar function in other viruses, and these may be susceptible to similar antiviral agents.

Influenza virus M2 protein has ion channel activity

The influenza virus M2 protein was expressed in Xenopus laevis oocytes and shown to have an associated ion channel activity selective for monovalent ions. The anti-influenza virus drug amantadine hydrochloride significantly attenuated the inward current induced by hyperpolarization of oocyte membranes. Mutations in the M2 membrane-spanning domain that confer viral resistance to amantadine produced currents that were resistant to the drug. Analysis of the currents of these altered M2 proteins suggests that the channel pore is formed by the transmembrane domain of the M2 protein. The wild-type M2 channel was found to be regulated by pH. The wild-type M2 ion channel activity is proposed to have a pivotal role in the biology of influenza virus infection.

Simian virus 5 membrane protein maturation: expression in virus-infected cells and from a eukaryotic vector

Properties of the membrane protein (M) of the paramyxovirus simian virus 5 (SV5) isolated from purified SV5 virions, in SV5-infected cells or when expressed from cDNA using a eukaryotic vector (SV40-M) were examined. Kinetic (pulse-chase radiolabeling) studies showed that M protein expressed in SV5-infected and SV40-M recombinant virus-infected cells underwent maturation, detectable as time-dependent acquisition of reactivity with anti-M protein monoclonal antibodies. Kinetic studies using radiolabeled phosphate and studies with the alkylating agent N-ethylmaleimide indicated that the antigenic maturation of the M protein was not due to phosphorylation or disulfide bond formation, respectively. Immunofluorescent antibody staining studies showed a significant difference in staining patterns between SV40-M recombinant virus-infected cells and SV5-infected cells. SV40-M recombinant virus-infected cells exhibited an intensely staining cytoplasmic fibrillar network, whereas in SV5-infected cells, villar and some small granular structures were the only strongly staining structures.

Diversity of coding strategies in influenza viruses

Influenza viruses have exploited a variety of strategies to increase their genome coding capacities. These include unspliced, spliced, alternatively spliced and bicistronic mRNAs, translation from overlapping reading frames and a coupled stop-start translation of tandem cistrons.

Topology of eukaryotic type II membrane proteins: importance of N-terminal positively charged residues flanking the hydrophobic domain

We have tested the role of different charged residues flanking the sides of the signal/anchor (S/A) domain of a eukaryotic type II (N(cyt)C(exo)) integral membrane protein in determining its topology. The removal of positively charged residues on the N-terminal side of the S/A yields proteins with an inverted topology, while the addition of positively charged residues to only the C-terminal side has very little effect on orientation. Expression of chimeric proteins composed of domains from a type II protein (HN) and the oppositely oriented membrane protein M2 indicates that the HN N-terminal domain is sufficient to confer a type II topology and that the M2 N-terminal ectodomain can direct a type II topology when modified by adding positively charged residues. These data suggest that eukaryotic membrane protein topology is governed by the presence or absence of an N-terminal signal for retention in the cytoplasm that is composed in part of positive charges.

Structural characteristics of the M2 protein of influenza A viruses: evidence that it forms a tetrameric channel

The evidence presented shows that the M2 protein of influenza A viruses exists in infected cells as a homotetramer composed of two disulfide-linked dimers held together by noncovalent interactions. The amphiphilic nature of the transmembrane alpha-helical domain is consistent with the protein forming a transmembrane channel with which amantadine, the specific anti-influenza A drug, interacts. Together these features provide a structural basis for the hypothesis that M2 has a proton translocation function capable of regulating the pH of vesicles of the trans-Golgi network, a role important in promoting the correct maturation of the hemagglutinin glycoprotein.

Two point mutations in the transmembrane domain of P68gag-ros inactive its transforming activity and cause a delay in membrane association

The transforming protein of the avian sarcoma virus UR2 is a 68-kDa transmembrane tyrosine protein kinase. We examined the relationship between membrane localization and transforming activity of P68 by changing Val-168-Val-169 in its hydrophobic domain into Asp-168-Glu-169. The resulting transmembrane (TM) mutant (P68TM) lost transforming activity toward chicken embryo fibroblasts (CEF). We found that the mutant protein was expressed and rapidly degraded into a smaller form which was still membrane associated and kinase active. The instability of the TM mutant protein is a phenomenon only manifested in CEF, because the same mutant protein was expressed with efficiency and stability similar to those of the wild-type protein in a transient expression system in COS cells. However, there are several differences between the wild-type and the TM mutant proteins in COS cells. The wild-type protein is more heavily phosphorylated and associated with membrane fractions in a cotranslational manner. It is enzymatically active when recovered from membrane fractions. The TM mutant protein is less phosphorylated, more labile toward protease degradation, and delayed in membrane association, with a lag period of 30 min or longer, and has little kinase activity when recovered from membrane fractions. Most of the kinase-active TM mutant protein was found in the cytosol fractions. Despite the delay, most of the TM protein in COS cells was found to be membrane associated, and its orientation on the cell surface was similar to that of the wild-type protein. It is probable that loss of the CEF-transforming activity of the TM mutant protein is due to its susceptibility to protease degradation resulting from improper membrane association of the newly synthesized product. The differences in the kinetics of membrane association and the distribution of kinase activity in COS cells might not be directly applicable in explaining the inability of the TM mutant to transform CEF but are intriguing as regards protein biosynthesis and translocation. The difference between CEF and COS cells implies that different factors or pathways are involved in the biosynthesis and processing of the TM mutant protein in these two cellular environments. Changes of P68TM in the kinetics of membrane association indicate that the transmembrane domain of ros, besides functioning as a membrane anchor, also plays a role in directing initial membrane association.

Sequence and crystallization of influenza virus B/Beijing/1/87 neuraminidase

Influenza B/Beijing/1/87 neuraminidase heads were isolated from virus via trypsin digestion and characterized by PAGE, N-terminal sequencing, electron microscopy, and enzyme activity. The heads were crystallized into two crystal forms; tetragonal plates, like other neuraminidase crystals described before, that diffract to medium resolution (3 A) and a new form consisting of trigonal prisms or needles that diffract to high resolution (at least 2 A). The gene segment coding for neuraminidase was sequenced and compared with the neuraminidase sequence of B/Lee/40. The deduced amino acid sequences for neuraminidase showed only a 7% difference, whereas those for the NB proteins differed by 20%.

Antigenic, sequence, and crystal variation in influenza B neuraminidase

The neuraminidase (NA) genes of influenza B viruses B/Maryland/59, B/Hong Kong/8/73, B/Singapore/222/79, B/Oregon/5/80, B/USSR/100/83, B/Victoria/3/85, B/Leningrad/179/86, B/Memphis/6/86, and B/Memphis/3/89 have been sequenced. The deduced amino acid sequences show high variability in the stalk domain of the NA, but a surprising degree of sequence conservation in the head region which carries all the antigenic and enzyme activity. The variable region coding for the neuraminidase stalk also translates into a variable section in the overlapping NB polypeptide, which is coded from a second reading frame that overlaps the first 100 amino acids of NA. The influenza B NAs are antigenically distinguishable with monoclonal antibodies in neuraminidase-inhibition tests, even when there is only one amino acid sequence difference. However, seven of nine escape mutants selected with monoclonal antibodies were distinguished only by the antibody used for selection. When NA heads of influenza B viruses are crystallized, there are remarkable differences in crystal morphology between neuraminidases which have very few sequence changes.

The neuraminidase of influenza virus

It is the enzyme neuraminidase, projecting from the surface of influenza virus particles, which allows the virus to leave infected cells and spread in the body. Antibodies which inhibit the enzyme limit the infection, but antigenic variation of the neuraminidase renders it ineffective in a vaccine. This article describes the crystal structure of influenza virus neuraminidase, information about the active site which may lead to development of specific and effective inhibitors of the enzyme, and the structure of epitopes (antigenic determinants) on the neuraminidase. The 3-dimensional structure of the epitopes was obtained by X-ray diffraction methods using crystals of neuraminidase complexed with monoclonal antibody Fab fragments. Escape mutants, selected by growing virus in the presence of monoclonal antibodies to the neuraminidase, possess single amino acid sequence changes. The crystal structure of two mutants showed that the change in structure was restricted to that particular sidechain, but the change in the epitope was sufficient to abolish antibody binding even though it is known in one case that 21 other amino acids on the neuraminidase are in contact with the antibody.

Topogenic signals in integral membrane proteins

Integral membrane proteins are characterized by long apolar segments that cross the lipid bilayer. Polar domains flanking these apolar segments have a more balanced amino acid composition, typical for soluble proteins. We show that the apolar segments from three different kinds of membrane-assembly signals do not differ significantly in amino acid content, but that the inside/outside location of the polar domains correlates strongly with their content of arginyl and lysyl residues, not only for bacterial inner-membrane proteins, but also for eukaryotic.proteins from the endoplasmic reticulum, the plasma membrane, the inner mitochondrial membrane, and the chloroplast thylakoid membrane. A positive-inside rule thus seems to apply universally to all integral membrane proteins, with apolar regions targeting for membrane integration and charged residues providing the topological information.

Transcending the impenetrable: how proteins come to terms with membranes

In the living cell, proteins are efficiently sorted to a whole range of subcellular compartments. In many cases, sorting specificity is mediated by short 'sorting signals' attached either permanently or transiently to the protein. At long last, a fairly coherent picture of the design and function of many such sorting signals is beginning to emerge.