John O. Thomas, Ph.D.

Molecular dynamics studies of the Nafion, Dow and Aciplex fuel-cell polymer membrane systems
Brandell, Daniel; Karo, Jaanus; Liivat, Anti; Thomas, John O
2007 Oct;13(10):1039-1046, Journal of molecular modeling
The Nafion, Dow and Aciplex systems--where the prime differences lies in the side-chain length--have been studied by molecular dynamics (MD) simulation under standard pressure and temperature conditions for two different levels of hydration: 5 and 15 water molecules per (H)SO(3) end-group. Structural features such as water clustering, water-channel dimensions and topology, and the dynamics of the hydronium ions and water molecules have all been analysed in relation to the dynamical properties of the polymer backbone and side-chains. It is generally found that mobility is promoted by a high water content, with the side-chains participating actively in the H(3)O(+)/H(2)O transport mechanism. Nafion, whose side-chain length is intermediate of the three polymers studied, is found to have the most mobile polymer side-chains at the higher level of hydration, suggesting that there could be an optimal side-chain length in these systems. There are also some indications that the water-channel network connectivity is optimal for high water-content Nafion system, and that this could explain why Nafion appears to exhibit the most favourable overall hydronium/water mobility
— id: 95001, year: 2007, vol: 13, page: 1039, stat: Journal Article,

Development of a force field for Li(2)SiF(6)
Liivat, Anti; Aabloo, Alvo; Thomas, John O
2005 May;26(7):716-724, Journal of computational chemistry
A force field has been developed for Li(2)SiF(6) for subsequent use in Molecular Dynamics (MD) simulations involving Li(+) and SiF(2-) (6) ions in a polymer electrolyte host. Both ab initio calculations and available empirical data have been used. The force field has been verified in simulations of the crystal structure of Li(2)SiF(6) in two different space groups: P321 and P3(-)m1. The use of MD simulation to assess the correct space group for Li(2)SiF(6) shows that it is probably P321
— id: 95002, year: 2005, vol: 26, page: 716, stat: Journal Article,

Li(3+delta)V6O13: a short-range-ordered lithium insertion mechanism
Howing, Jonas; Gustafsson, Torbjorn; Thomas, John O
2004 Aug;60(Pt 4):382-387, Acta crystallographica. Section B, Structural science
The structures of Li3V6O13 and Li(3+delta)V6O13, delta approximately 0.3, have been determined by single-crystal X-ray diffraction. Both compounds have the space group C2/m, with very similar cell parameters. In Li3V6O13, the Li atoms are found in the Wyckoff positions 4(i) and 2(b) with multiplicities of four and two, respectively. Since Li3V6O13 exhibits no superstructure reflections, it is concluded that Li3V6O13 contains one disordered lithium ion in an otherwise ordered centrosymmetric structure. On inserting more lithium into the structure, the Li(3+delta)V6O13 phase is formed with the homogeneity range 0 < delta < 1. It is concluded that the site for the extra inserted lithium ion is closely coupled to the position of the disordered lithium ion in Li3V6O13. A mechanism for this behaviour and for the further formation of the Li6V6O13 end-phase in the LixV6O13 system is proposed
— id: 95003, year: 2004, vol: 60, page: 382, stat: Journal Article,

Lithium vanadate Li(3+x)V6O13 at low temperature
Howing, Jonas; Gustafsson, Torbjorn; Thomas, John O
2004 Jul;60(Pt 7):i66-i68, Acta crystallographica. Section C. Crystal structure
The structure of Li(3+x)V6O13 [x = 0.24 (3)] at 95 K has been solved and refined using single-crystal X-ray diffraction. The refined lithium content corresponds to two fully occupied Li sites and one partially occupied Li site. A doubling of the c axis is observed upon cooling from room temperature, and this change is associated with shifts of the V atoms. The resulting space group is C2/c. The Li disorder present in the Li3V6O13 phase at room temperature is also observed in the low-temperature phase reported here
— id: 95004, year: 2004, vol: 60, page: i66, stat: Journal Article,

Low-temperature structure of V6O13
Howing, Jonas; Gustafsson, Torbjorn; Thomas, John O
2003 Dec;59(Pt 6):747-752, Acta crystallographica. Section B, Structural science
The structure of the transition metal oxide V6O13, a potential cathode material in lithium-polymer batteries, has been studied at 95 K using single-crystal X-ray diffraction (XRD). A phase transition has been determined by differential scanning calorimetry (DSC) measurements to occur at 153 K, with a heat of transition of -1.98 kJ mol(-1). In this low-temperature phase, the V and O atoms move by up to 0.21 A out of the mirror plane they occupy in the room-temperature structure. It is concluded that the earlier reported space group P2(1)/a [Kawada et al. (1978). Acta Cryst. B34, 1037-1039] is incorrect and that a more appropriate choice of space group is Pc
— id: 95005, year: 2003, vol: 59, page: 747, stat: Journal Article,

A cytoplasmic chaperonin that catalyzes beta-actin folding
Gao Y; Thomas JO; Chow RL; Lee GH; Cowan NJ
1992 Jun 12;69(6):1043-1050, Cell
We have isolated a cytoplasmic chaperonin based on its ability to catalyze the folding of denatured beta-actin. The cytoplasmic chaperonin is organized as a multisubunit toroid and requires Mg2+ and ATP for activity. The folding reaction proceeds via the rapid ATP-independent formation of a binary complex, followed by a slower ATP-dependent release of the native product. Electron microscopic observations reveal a striking structural change that occurs upon addition of Mg2+ and ATP. The eukaryotic cytoplasm thus contains a chaperonin that is functionally analagous to its prokaryotic, mitochondrial, and chloroplastic counterparts
— id: 13562, year: 1992, vol: 69, page: 1043, stat: Journal Article,

Intracellular distribution of a nuclear localization signal binding protein
Li R; Shi Y; Thomas JO
1992 Oct;202(2):355-365, Experimental cell research
The transport of proteins into the nucleus requires the recognition of a nuclear localization signal sequence. Several proteins that interact with these sequences have been identified, including one of about 66 kDa. We have prepared antibodies that recognize the 66-kDa nuclear localization signal binding protein (NLSBP) and inhibit nuclear localization in vitro. By immunofluorescence, it is seen that the NLSBP is predominantly cytoplasmic and is distributed peripherally around the nucleus and the microtubule organizing center. There is also a weak punctate staining of the surface of the nucleus. Methanol-fixed cells can also be stained directly with fluorescently labeled karyophilic proteins. These stains reveal the same cytoplasmic structures as anti-NLSBP. The expression of the NLSBP is growth dependent. When cells grown to confluence are examined, the cytoplasmic staining is greatly reduced, leaving the punctate nuclear staining as the predominant feature. In serum-starved cells, very little staining of either the cytoplasm or the nucleus can be seen. Upon simulation by the addition of serum, the original cytoplasmic and nuclear envelope staining is restored. Cells grown in the presence of colchicine or taxol have an altered NLSBP distribution but apparently normal cytoplasmic nuclear transport
— id: 13428, year: 1992, vol: 202, page: 355, stat: Journal Article,

The transport of proteins into the nucleus requires the 70-kilodalton heat shock protein or its cytosolic cognate
Shi Y; Thomas JO
1992 May;12(5):2186-2192, Molecular & cellular biology
The 70-kDa heat shock protein hsp70 and its constitutively expressed cognate, hsc70, are abundant proteins implicated in a number of cellular processes. When a permeabilized cell system for examining the transport of proteins into the nucleus is depleted of hsc70 and hsp70, either by affinity chromatography on ATP-agarose or with antibodies against these proteins, nuclear transport activity is lost. Full activity is restored by the addition of HeLa proteins that bind to ATP-agarose. hsc70 and hsp70 are the active factors, since activity is also fully restored by the addition of either recombinant hsc70 or hsp70 which has been bacterially expressed and highly purified. The restoration of activity is saturable. The transport system requires other cytosolic factors as well, including at least one protein that is sensitive to inactivation by N-ethylmaleimide, but neither hsc70 nor hsp70 is the sensitive protein
— id: 8280, year: 1992, vol: 12, page: 2186, stat: Journal Article,

Mammalian mitochondrial chaperonin 60 functions as a single toroidal ring
Viitanen PV; Lorimer GH; Seetharam R; Gupta RS; Oppenheim J; Thomas JO; Cowan NJ
1992 Jan 15;267(2):695-698, Journal of biological chemistry
Chaperonins are thought to participate in the process of protein folding in bacteria and in eukaryotic mitochondria and chloroplasts. While some chaperonins are relatively well characterized, the structures of the mammalian chaperonins are unknown. We have expressed a mammalian mitochondrial chaperonin 60 in Escherichia coli and purified the recombinant protein to homogeneity. Structural and biochemical analyses of this protein establish a single toroidal structure of seven subunits, in contrast to the homologous bacterial, fungal, and plant chaperonin 60s, which have double toroidal structures comprising two layers of seven identical subjects each. The recombinant mammalian chaperonin 60, together with the mammalian chaperonin 10 (but not with bacterial chaperonin 10), facilitates the formation of catalytically active ribulose-bisphosphate carboxylase from an unfolded state in the presence of K+ and MgATP. Analysis of the partial reactions involved in this in vitro reconstitution reveals that the single toroid of chaperonin 60 can form stable complexes with both unfolded or partially folded [35S]ribulose-bisphosphate carboxylase and mitochondrial (but not bacterial) chaperonin 10 in the presence of MgATP. We conclude that the minimal functional unit of chaperonin 60 is a single hepatmeric toroid
— id: 8274, year: 1992, vol: 267, page: 695, stat: Journal Article,

Physical methods for characterization of heterogeneous nuclear ribonucleoprotein complexes
Schoneich, J T; Thomas, J O
1990 ;181:307-317, Methods in enzymology
— id: 145525, year: 1990, vol: 181, page: 307, stat: Journal Article,

Identification of a human protein that interacts with nuclear localization signals
Li RH; Thomas JO
1989 Dec;109(6 Pt 1):2623-2632, Journal of cell biology
Through a series of label transfer experiments, we have identified a HeLa cell nuclear protein that interacts with nuclear localization signals (NLSs). The protein has a molecular weight of 66,000 and an isoelectric point of approximately 6. It associates with a synthetic peptide that contains the SV-40 T antigen NLS peptide but not with an analogous peptide in which an asparagine is substituted for an essential lysine (un-NLS peptide). In addition to these peptides, several proteins have been tested as label donors. With the proteins, there is a correlation between nuclear localization (assayed with lysolecithin-permeabilized cells) and label transfer to the 66-kD protein. The NLS peptide (but not the un-NLS peptide) competes with the proteins in label transfer experiments, but neither wheat germ agglutinin nor ATP has an effect. These results suggest that the 66-kD protein functions as an NLS receptor in the first step of nuclear localization. In the course of this work, we have observed that the Staphylococcus aureus protein A is a strongly karyophilic protein. Its dramatic nuclear localization properties suggest that it may have multiple copies of an NLS
— id: 8279, year: 1989, vol: 109, page: 2623, stat: Journal Article,

Specific immune responses in Lyme borreliosis. Characterization of T cell and B cell responses to Borrelia burgdorferi
Dattwyler RJ; Volkman DJ; Halperin JJ; Luft BJ; Thomas J; Golightly MG
1988 ;539:93-102, Annals of the New York Academy of Sciences
— id: 65098, year: 1988, vol: 539, page: 93, stat: Journal Article,

Seronegative Lyme disease. Dissociation of specific T- and B-lymphocyte responses to Borrelia burgdorferi
Dattwyler RJ; Volkman DJ; Luft BJ; Halperin JJ; Thomas J; Golightly MG
1988 Dec 1;319(22):1441-1446, New England journal of medicine
The diagnosis of Lyme disease often depends on the measurement of serum antibodies to Borrelia burgdorferi, the spirochete that causes this disorder. Although prompt treatment with antibiotics may abrogate the antibody response to the infection, symptoms persist in some patients. We studied 17 patients who had presented with acute Lyme disease and received prompt treatment with oral antibiotics, but in whom chronic Lyme disease subsequently developed. Although these patients had clinically active disease, none had diagnostic levels of antibodies to B. burgdorferi on either a standard enzyme-linked immunosorbent assay or immunofluorescence assay. On Western blot analysis, the level of immunoglobulin reactivity against B. burgdorferi in serum from these patients was no greater than that in serum from normal controls. The patients had a vigorous T-cell proliferative response to whole B. burgdorferi, with a mean ( +/- SEM) stimulation index of 17.8 +/- 3.3, similar to that (15.8 +/- 3.2) in 18 patients with chronic Lyme disease who had detectable antibodies. The T-cell response of both groups was greater than that of a control group of healthy subjects (3.1 +/- 0.5; P less than 0.001). We conclude that the presence of chronic Lyme disease cannot be excluded by the absence of antibodies against B. burgdorferi and that a specific T-cell blastogenic response to B. burgdorferi is evidence of infection in seronegative patients with clinical indications of chronic Lyme disease
— id: 65096, year: 1988, vol: 319, page: 1441, stat: Journal Article,

DECAY ACCELERATING FACTOR DIFFUSES RAPIDLY ON HELAAE CELL- SURFACES
Thomas, J; Webb, W; Davitz, MA; Nussenzweig, V
1987 Feb;51(2):A522-A522, Biophysical journal
— id: 31414, year: 1987, vol: 51, page: A522, stat: Journal Article,

A cDNA clone of the hnRNP C proteins and its homology with the single-stranded DNA binding protein UP2
Lahiri, D K; Thomas, J O
1986 May 27;14(10):4077-4094, Nucleic acids research
A cDNA clone which expresses a protein that cross-reacts immunologically with the human C1 and C2 hnRNP core proteins has been isolated. The clone was selected by a sensitive immunochemical assay employing an avidin-biotin complex for detection, and identified as a clone for the hnRNP C proteins by a highly sensitive antibody select assay that is described here. The clone contains 677 nucleotides, and, as shown by northern blotting, is derived from a 1.5 Kb poly(A)+ mRNA. There are regions of strong homology between the human and mouse genes, weak homology is seen with chicken DNA, and very little, if any, homology can be detected with Drosophila, Artemia, sea urchin, or yeast DNAs. Two peptides (a total of 24 amino acids) of the calf thymus single-stranded DNA binding protein UP2 show perfect homology with the deduced amino acid sequence of the clone, suggesting that UP2 is related to the hnRNP C proteins. There is also a region that has a sequence very similar to two regions of the single-stranded DNA binding protein UP1 that contain proposed DNA binding sites
— id: 145526, year: 1986, vol: 14, page: 4077, stat: Journal Article,

The fate of heterogeneous nuclear ribonucleoprotein complexes during mitosis
Lahiri, D K; Thomas, J O
1985 Jan 10;260(1):598-603, Journal of biological chemistry
Using immunochemical techniques, we have examined the macromolecular state of association of the major heterogeneous nuclear ribonucleoprotein (hnRNP) core proteins in mitotic HeLa cells. We find that these proteins are not free but are associated with high-molecular-weight RNA in the form of particles that sediment as a broad band between 80 and 200 S. We have termed these complexes MhnRNP for mitotic hnRNP protein-containing particles. Their quantity, composition, sedimentation coefficients, buoyant density, and sensitivity to dissociating conditions suggest that they are closely related to the hnRNP complexes of interphase cells and may represent hnRNP complexes containing unprocessed or partially processed heterogeneous nuclear RNA that have been released into the cytoplasm during mitosis. Exogenously added RNA does not associate with the MhnRNP nor does it compete for the major MhnRNP proteins. The MhnRNP remain distinct from other ribonucleoprotein complexes and do not associate with ribosomes even though these structures are not separated by a nuclear envelope during mitosis
— id: 145527, year: 1985, vol: 260, page: 598, stat: Journal Article,

Model investigations on the structure of heterogeneous nuclear ribonucleoproteins
Glowacka SK; Raziuddin; Thomas JO; Szer W
1984 ;31(1):103-114, Acta biochemica polonica
Protein HD40 , an RNA-helix destabilizing protein (Mr 40 000) is the major component of 30S heterogeneous nuclear ribonucleoprotein particles (hnRNP) from Artemia salina. The physical properties and the amino acid composition of HD40 are analogous to those of a group of well conserved core hnRNP proteins of higher eukaryotes. HD40 binds to and disrupts the secondary structure of single-stranded polynucleotides and forms extended nucleoprotein filaments at a stoichiometry of one protein per 12-15 nucleotides. The addition of a saturating amount of HD40 (one protein per 8 nucleotides) converts the filaments into bead-like complexes that are similar in properties and appearance to native hnRNP. To gain an understanding of the structure of hnRNP, we have used analytical ultracentrifugation and electron microscopy to investigate the structure of beaded complexes reconstituted from HD40 and poly(A)n of defined sizes. A complex containing 160 nucleotides forms a disc that is 3 nm high by 18 nm in diameter. At n less than 160 the complexes form sectors of the disc: 40 nucleotides give rise to a quarter of a disc, 80 nucleotides, half a disc, etc. At n greater than 160, the additional nucleoprotein elements may either initiate the formation of a second disc adjacent to the first or stack on top of the first disc to form a 6 nm high helix with a diameter of 18 nm. A single 'bead' sediments at approximately 30S and contains an average of approximately 300 nucleotides and 1.8 turns of the helix. Native hnRNP particles from A. salina sediment at about 30S, have a diameter of 18-20 nm, and contain RNA fragments 180 to 400 nucleotides long
— id: 64568, year: 1984, vol: 31, page: 103, stat: Journal Article,

Isolation of a minor species of actin from the nuclei of Acanthamoeba castellanii
Kumar A; Raziuddin; Finlay TH; Thomas JO; Szer W
1984 Dec 18;23(26):6753-6757, Biochemistry
Actin was extracted from isolated nuclei of Acanthamoeba castellanii and purified to homogeneity under nondenaturing conditions by diethylaminoethylcellulose and Sephadex G-100 chromatography. The pure protein has the same molecular weight as cytoplasmic Acanthamoeba actin and a very similar amino acid composition. Isoelectrofocusing shows that nuclear actin is slightly more acidic than the major cytoplasmic species, and comparative analysis of peptides from tryptic and cyanogen bromide digests shows that both actins are very similar but not chemically identical. In an assay that is specific for most actins, the inhibition of DNase I through the formation of a 1:1 G-actin-DNase I complex, the nuclear and cytoplasmic actins are equally effective. By use of a similar procedure for the purification of both actins, it is estimated that the amount of nuclear actin is about 1.5% of the amount of cytoplasmic actin, a major protein of the amoeba. It is concluded that a minor isoelectric species of actin associates selectively with the nuclei of A. castellanii
— id: 17473, year: 1984, vol: 23, page: 6753, stat: Journal Article,

Structure of complexes between a major protein of heterogeneous nuclear ribonucleoprotein particles and polyribonucleotides
Thomas JO; Glowacka SK; Szer W
1983 Dec 25;171(4):439-455, Journal of molecular biology
We have investigated the structure of complexes formed between a series of poly(A)n (n = 30 to 480) and HD40 (helix-destabilizing protein, molecular weight of 40,000), the major protein component of 30 S heterogeneous nuclear ribonucleoprotein particles (hnRNP) from the brine shrimp Artemia salina. Protein HD40 is similar to corresponding hnRNP proteins from higher eukaryotes and the complexes it forms with single-stranded nucleic acids are strikingly similar to the native 'beads-on-a-string' structure of hnRNP. Using analytical ultracentrifugation and electron microscopy we find: (1) complexes formed between HD40 and long ribohomopolymers also have a beads-on-a-string structure, showing that the ability to form this structure is an inherent property of HD40, and is not dependent on any structural features of natural RNA; (2) complexes between HD40 and poly(A)160 form disks that are about 3 nm high by 18 nm in diameter and contain 20 HD40 molecules; (3) complexes of HD40 with poly(A)n with fewer than 160 nucleotides form sectors of a disk: 40 nucleotides give rise to a quarter of a disk, 80 nucleotides, half a disk, etc. The molecular weights increase with the size of poly(A)n at the rate of 5300 per nucleotide, a stoichiometry of eight nucleotides per HD40; (4) as the size of the poly(A)n increases beyond 160 nucleotides, the additional nucleoprotein elements may either initiate the formation of a second disk adjacent to the first or stack on top of the first disk to form a 6 nm high helix with a diameter of 18 nm. Based on these results, we propose that the existence of lateral protein-protein interactions that produce the basic 3 nm X 18 nm disk, combined with the marginal stability of the helix result in (a) interruptions of the helix that give rise to the beads-on-a-string appearance of the complexes, and (b) inherent heterogeneity of individual 'beads' which may contain one or more turns of the helix. From measurements of HD40 complexes with coliphage MS2 RNA, phi X174 viral DNA as well as with the homopolymers, a bead is estimated to contain an average of approximately 300 nucleotides; approximately 1 X 8 turns of the helix
— id: 17474, year: 1983, vol: 171, page: 439, stat: Journal Article,

The effect of prostaglandins on the multiplication and cell-to-cell spread of herpes simplex virus type 2 in vitro
Baker, D A; Thomas, J; Epstein, J; Possilico, D; Stone, M L
1982 Oct 1;144(3):346-349, American journal of obstetrics & gynecology
Herpes simplex virus type 2 (HSV-2) after infecting an individual has the ability to remain latent in nervous tissues. The factors that control herpesvirus infection, latency, and reactivation are poorly understood. Fever, menstruation, emotional stress, exposure to sunlight, and surgical resection have been associated with activation of latent herpes. The situations which activate latent herpes are associated with a local or systemic rise in prostaglandins. The data presented show that prostaglandin F2 alpha (PGF2 alpha) and E2 (PGE2) enhanced cell-to-cell spread of HSV-2 in an in vitro model. Ibuprofen, a prostaglandin inhibitor, suppressed HSV-2 multiplication as well as cell-to-cell spread. Prostaglandins may play an important role in herpesvirus infections and latency
— id: 121482, year: 1982, vol: 144, page: 346, stat: Journal Article,

Nucleic acid binding properties of major proteins from the heterogeneous nuclear ribonucleoproteins of wheat
Raziuddin; Thomas JO; Szer W
1982 Dec 11;10(23):7777-7789, Nucleic acids research
Glycine-rich core hnRNP proteins purified from wheat bind tightly to single-stranded but not to double-stranded nucleic acids with a preference for natural RNA over single-stranded DNA. Binding results in i) a progressive disruption of the residual secondary structure of the polynucleotide and the formation of an extended nucleoprotein filament until a protein to polynucleotide weight ratio of about 5:1 is attained. As more protein is added, this is followed by ii) the formation of globular structures along the polynucleotide chain with a concomitant reduction in the contour length of the nucleoprotein complex. These two features of the interaction--unwinding and condensation into beads--are analogous to the previously described behavior of the major glycine-rich core hnRNP protein from Artemia salina (Thomas et al. (1981) Proc. Natl. Acad. Sci. USA 78, 2888) and may represent the basic functional properties of this relatively well conserved group of nuclear proteins
— id: 17477, year: 1982, vol: 10, page: 7777, stat: Journal Article,

RNA-helix-destabilizing proteins
Thomas JO; Szer W
1982 ;27(23):157-187, Progress in nucleic acid research & molecular biology
— id: 17478, year: 1982, vol: 27, page: 157, stat: Journal Article,

IDENTIFICATION AND PROPERTIES OF A STRUCTURE-FORMING PROTEIN OF HNRNP FROM ARTEMIA-SALINA
Raziuddin; Thomas, JO; Szer, W
1981 ;40(6):1571-1571, Federation Proceedings (Federation of American Societies for Experimental Biology)
— id: 30251, year: 1981, vol: 40, page: 1571, stat: Journal Article,

A RNA helix-destabilizing protein is a major component of Artemia salina nuclear ribonucleoproteins
Thomas JO; Raziuddin; Sobota A; Boublik M; Szer W
1981 May;78(5):2888-2892, Proceedings of the National Academy of Sciences of the United States of America
A major component of 30S heterogeneous nuclear ribonucleoprotein (hnRNP) particles from Artemia salina is HD40, a protein that has been characterized as a RNA helix-destabilizing protein [Marvil, D. K., Nowak, L. & Szer, W. (1980) J. Biol. Chem. 255, 6466-6472; Nowak, L., Marvil, D. K., Thomas, J. O., Boublik, M. & Szer, W. (1980) J. Biol. Chem. 255, 6473-6478]. HD40 binds to and disrupts the secondary structure of nuclear RNA fragments isolated from 30S hnRNP with a stoichiometry of one protein per 10-12 nucleotides. The addition of HD40 in excess of this ratio results in the formation of bead-like HD4-nuclear RNA complexes that are similar in properties and appearance to native 30S hnRNP particles. The heterogeneous nuclear RNA (hnRNA) in the HD40-hnRNA complexes is unstacked and unfolded to about the same extent as the RNA in the native 30S hnRNP particles. HD40 is strikingly similar in molecular weight (40,000) and amino acid composition (no cysteine, high glycine, presence of dimethylarginine, and blocked NH2 terminus) to eukaryotic hnRNP proteins isolated from many cell types. HD40 can be separated into three isoelectric species with basic pIs, which appears to be posttranslational modifications of a single polypeptide chain
— id: 17479, year: 1981, vol: 78, page: 2888, stat: Journal Article,

Lectins in the U.S. Diet. Isolation and characterization of a lectin from the tomato (Lycopersicon esculentum)
Nachbar MS; Oppenheim JD; Thomas JO
1980 Mar 10;255(5):2056-2061, Journal of biological chemistry
— id: 18946, year: 1980, vol: 255, page: 2056, stat: Journal Article,

A single-stranded nucleic acid-binding protein from Artemia salina. II. Interaction with nucleic acids
Nowak L; Marvil DK; Thomas JO; Boublik M; Szer W
1980 Jul 10;255(13):6473-6478, Journal of biological chemistry
A helix-destabilizing protein, HD40 (Mr 40,000), isolated from the cytoplasm of Artemia salina (Marvil, D.K., Nowak, L., and Szer, W. (1980) J. Biol. Chem. 255, 6466-6472) stoichiometrically disrupts the secondary structures of synthetic single-stranded and helical polynucleotides (e.g. poly(rA), poly(dA), poly(rC), poly(dC), and poly(rU)) as well as those of natural polynucleotides (e.g. MS2 RNA and phi X174 viral DNA). The conformations of double-stranded DNA and double- or triple-stranded synthetic polynucleotides are not affected by the protein. Formation of duplexes, e.g. poly(rA . rU), is prevented by HD40 at 25 to 50 mM but not at 100 to 140 mM NaCl. The unwinding of the residual secondary structure of RNA and DNA by HD40 is not highly cooperative and has a stoichiometry of one HD40 per 12 to 15 nucleotides. The addition of HD40 in excess of 1 molecule per 12 to 15 nucleotides results in the cooperative formation of distinct bead-like structures along the nucleic acid strand. The beads are about 20 nm in diameter with a center to center distance of about 40 nm. The appearance of the beads is not accompanied by any spectral changes (CD and UV) beyond those obtained at a stoichiometry of one HD40 molecule per 12 to 15 nucleotides
— id: 17480, year: 1980, vol: 255, page: 6473, stat: Journal Article,

A MAJOR COMPONENT OF MESSENGER RNP FROM ARTEMIA-SALINA IS A HELIX-DESTABILIZING PROTEIN
Thomas, JO; Sobota, A; Szer, W
1980 ;39(6):1876-1876, Federation Proceedings (Federation of American Societies for Experimental Biology)
— id: 28108, year: 1980, vol: 39, page: 1876, stat: Journal Article,

Nucleic acid binding and unfolding properties of ribosomal protein S1 and the derivatives S1-F1 and m1-S1
Thomas JO; Boublik M; Szer W; Subramanian AR
1979 Dec;102(1):309-314, European journal of biochemistry
The nucleic acid binding and unwinding properties of wild-type Escherichia coli ribosomal protein S1 have been compared to those of a mutant form and a large trypsin-resistant fragment, both reported recently [J. Mol. Biol. 127, 41-45 (1979) and J. Biol. Chem. 254, 4309-4312 (1979). The mutant (m1-S1) contains 77% and the fragment (S1-F1) 66% of the polypeptide chain length (approximately 600 amino acid residues) of protein S1. The mutant is active in protein synthesis in vitro; the fragment, although retaining one or more of the functional domains of S1, is inactive in protein synthesis. We find that m1-S1 is is almost as effective as S1 in binding to poly(rU), phage MS2 RNA and simian virus 40 (SV40) DNA, and in unfolding poly(rU) and the helical structures present in MS2 RNA and phi X174 viral DNA. S1-F1, however, binds to poly(rU) and denatured SV40 DNA, but not to MS2 RNA. It unfolds neither poly(rU), nor the residual secondary structure of MS2 RNA or phi X174 viral DNA. Thus, there appears to be a correlation between the loss in ability of S1 to unwind RNA and the loss in its ability to function in protein synthesis
— id: 17482, year: 1979, vol: 102, page: 309, stat: Journal Article,

Structure of single-stranded nucleic acids in the presence of ribosomal protein S1
Thomas JO; Kolb A; Szer W
1978 Aug 5;123(2):163-176, Journal of molecular biology
— id: 17485, year: 1978, vol: 123, page: 163, stat: Journal Article,

Altered arrangement of the DNA in injection-defective lambda bacteriophage
Thomas, J O; Sternberg, N; Weisberg, R
1978 Aug 5;123(2):149-161, Journal of molecular biology
— id: 145528, year: 1978, vol: 123, page: 149, stat: Journal Article,

Nucleic acid helix-unwinding properties of ribosomal protein S1 and the role of S1 in mRNA binding to ribosomes
Kolb A; Hermoso JM; Thomas JO; Szer W
1977 Jun;74(6):2379-2383, Proceedings of the National Academy of Sciences of the United States of America
The presence of ribosomal protein S1 in 30S ribosomes is indispensable for the formation of 30S initiation complexes with natural mRNA. The 30S subunits lacking S1 retain activity with AUG as mRNA and are also active in poly(rU)-directed binding of Phe-tRNA. Isolated protein S1 stoichiometrically disrupts the secondary structure of helical and stacked single-stranded polynucleotides and converts them into their fully or partially denatured forms. A mono-N-ethylmaleimide derivatives of S1 is nearly devoid of any RNA helix-unwinding properties but is readily incorporated into 30S subunits deficient in S1. The resulting N-ethylmaleimide-S1-containing 30S subunits are completely inactive in the binding of MS2 [3H]RNA and in the formation of an initiation complex with MS2 RNA as mRNA. They retain activity in the binding of the initiator fMet-tRNA in response to the trinucleotide AUG and in the binding of Phe-tRNA in response to poly(U). They also retain the capacity to bind 50S subunits and to form 70S couples. These results suggest that a correlation exists between the RNA helix-unwinding capacity of isolated S1 and the function of S1 in the ribosomal binding of natural mRNA when the protein becomes part of the 30S subunit
— id: 17486, year: 1977, vol: 74, page: 2379, stat: Journal Article,

Ribosomal protein S1 alters the ordered state of synthetic and natural polynucleotides
Szer W; Thomas JO; Kolb A
Nucleic acid-protein recognition New York, Academic Press, 1977,
— id: 2593, year: 1977, vol: , page: 519, stat: Chapter,