Biology subjects

Jianxing Song

Publications and source records attributed to Jianxing Song.

7 recordsLinked to original sources

bioRxiv2016

Identification of a Zika NS2B-NS3pro pocket susceptible to allosteric inhibition by small molecules including qucertin rich in edible plants

It has been recently estimated that one-third of the world population will be infected by Zika virus, but unfortunately so far there is no vaccine or medicine available. In particular, the special concern on the vaccine treatment to Zika and Dengue arising from antibody-dependent enhancement strongly emphasizes the irreplaceable role of its NS2B-NS3 protease (NS2B-NS3pro) as a target for anti-Zika drug discovery/design due to its absolutely-essential role in viral replication. Very recently we identified two small molecules inhibit Zika NS2B-NS3pro in non-competitive mode, with Ki values of 0.57 and 2.02 {micro}M respective for p-Nitrophenyl-p-guanidino benzoate and qucertin. Here, by molecular docking, we show that although one is designed compound while another is a natural product, both molecules bind to the same pocket on the back of the substrate-binding pocket of Zika NS2B-NS3pro. As the two inhibitors fundamentally differ from cn-716, the only known peptidomimetic boronic acid inhibitor in both structure scaffolds and inhibitory modes, our discovery might open up a new avenue for the future development of allosteric inhibitors, which is highly demanded to achieve therapeutic inhibition of flaviviral NS2B-NS3pro complexes. Furthermore, as qucertin is abundant in many vegetables and fruits such caper, lovage, tea and red onion, our results should benefit the public to immediately fight Zika virus.

Biophysics↗

bioRxiv2016

Unique properties of Zika NS2B-NS3pro complexes as decoded by experiments and MD simulations

Zika virus can be passed from a pregnant woman to her fetus, thus leading to birth defects including more than microcephaly. It has been recently estimated that one-third of the world population will be infected by Zika, but unfortunately no vaccine or medicine is available so far. Zika NS2B-NS3pro is essential for its replication and thus represents an attractive target for drug discovery/design. Here we characterized conformation, catalysis, inhibition and dynamics of linked and unlinked Zika NS2B-NS3pro complexes by both experiments and MD simulations. The results unveil the unique properties of Zika NS2B-NS3pro which are very different from Dengue one. Particularly, CD and NMR studies indicate that unlike Dengue, the C-terminal region of Zika NS2B with a significant sequence variation is highly disordered in the open conformation. Indeed, MD simulations reveal that up to 100 ns, the Dengue NS2B C-terminus constantly has close contacts with its NS3pro domain. By a sharp contrast, the Zika NS2B C-terminus loses the contacts with its NS3pro domain after 10 ns, further forming a short {beta}-sheet characteristic of the closed conformation at 30 ns. Furthermore, we found that a small molecule, previously identified as an active site inhibitor for other flaviviral NS2B-NS3pro, inhibited Zika NS2B-NS3pro potently in an allosteric manner. Our study provides the first insight into the dynamics of Zika NS2B-NS3pro and further deciphers that it is susceptible to allosteric inhibition, which thus bears critical implications for the future development of therapeutic allosteric inhibitors.

Biophysics↗

bioRxiv2016

Identification of quercetin from fruits to immediately fight Zika

Zika virus is spread mainly by the bite of an infected mosquito, which can be passed from a pregnant woman to her fetus, thus leading to birth defects including more than microcephaly. It has been recently estimated that one-third of the world population will be infected by Zika in the near future, but unfortunately so far there is no vaccine or medicine for Zika. In particular, the special concern on the vaccine treatment to Zika and Dengue arising from antibody-dependent enhancement strongly emphasizes the key role of its NS2B-NS3 protease (NS2B-NS3pro) as a target for anti-Zika drug discovery/design due to its absolutely-essential role in viral replication.\n\nIn response to the current global health emergency triggered by the Zika outbreak, we successfully obtained several active forms of Zika NS2B-NS3pro and further attempted to discover its inhibitors from eatable plants and traditional herbal medicines to immediately fight Zika. Here, for the first time, we discovered that quercetin, a flavonoid extensively existing in many fruits and vegetables, effectively inhibits Zika NS2B-NS3pro. We further quantify its inhibitory activity with IC50 of 26.0 {+/-} 0.1 {micro}M; and Ki of 23.0 {+/-} 1.3 {micro}M. As quercetin has been extensively found in fruits, vegetables, leaves and grains, our discovery would benefit the public to immediately fight Zika.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC=\"FIGDIR/small/074559_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (55K):\norg.highwire.dtl.DTLVardef@18e716dorg.highwire.dtl.DTLVardef@b8d5f6org.highwire.dtl.DTLVardef@e7206aorg.highwire.dtl.DTLVardef@11cf2_HPS_FORMAT_FIGEXP M_FIG C_FIG

Biochemistry↗

bioRxiv2016

Direct and Indirect Models for Protein Chemical Denaturation are Characteristic of Opposite Dynamic Properties

Two major models, namely direct and indirect models, have been proposed for the protein chemical denaturation but it remains challenging to experimentally demonstrate and distinguish between them. Here, by use of CD and NMR spectroscopy, we succeeded in differentiating the effects on a small but well-folded protein WW4, of GdmCl and NaSCN at diluted concentrations ([≥]200 mM). Both denaturants up to 200 mM have no alternation of its average structure but do reduce its thermodynamic stability to different degrees. Despite acting as the stronger denaturant, GdmCl only weakly interacts with amide protons, while NaSCN shows extensive interactions with both hydrophobic side chains and amide protons. Although both denaturants show no significant perturbation on overall ps-ns backbone dynamics of WW4, GdmCl suppresses while NaSCN enhances its s-ms backbone dynamics in a denaturant concentration dependent manner. Quantitative analysis reveals that although they dramatically raise exchange rates, GdmCl slightly increases while NaSCN reduces the population of the major conformational state. Our study represents the first report deciphering that GdmCl and NaSCN appear to destabilize a protein following two models respectively, which are characteristic of opposite s-ms dynamics.

Biophysics↗

bioRxiv2016

Unlocked capacity of proteins to attack membranes characteristic of aggregation: the evil for diseases and aging from Pandora’s box

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC=\"FIGDIR/small/071274_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (61K):\norg.highwire.dtl.DTLVardef@3e897borg.highwire.dtl.DTLVardef@1b429f6org.highwire.dtl.DTLVardef@12f0dbeorg.highwire.dtl.DTLVardef@2f5d8f_HPS_FORMAT_FIGEXP M_FIG C_FIG AbstractAggregation of specific proteins is characteristic of a large spectrum of human diseases including all neurodegenerative diseases, while aggregation of non-specific proteins has been now identified to be a biomarker for cellular aging down to Escherichia coli. Previously, as facilitated with our discovery in 2005 that \"completely insoluble\" proteins could be all solubilized in unsalted water [Song (2009) FEBS Lett. 583: 953], we found that the TDP-43 prion-like domain in fact contains an intrinsic membrane-interacting subdomain [Lim et al. [2016] PLoS Biol. 14, e1002338]. We decrypted that ALS-causing mutations/cofactor-depletion act to render the wellstructured folds of cytosolic VAPB-MSP domain and SOD1 into highly disordered states, thus becoming buffer-insoluble. Most surprisingly, this also unlocks the amphiphilic/hydrophobic regions universally exiting in proteins, which thus acquire a novel capacity in abnormally interacting with membranes [Qin et al. (2013) F1000Res 2-221.v2; Lim (2016) BBA-Biomembranes. 1858: 2223]. Here we aimed extend our discovery to address two fundamental questions: 1) why many E. coli proteins become aggregated in aging; and 2) whether aggregation-prone proteins can also acquire a novel capacity in interacting with membranes; by dissecting the 557-residue S1 ribosomal protein into 7 fragments to disrupt its 6 S1 folds, followed by extensive CD and NMR characterizations. The results reveal that we have successfully eliminated all 6 S1 folds and fragment 4 becomes highly disordered and thus buffer-insoluble. Most strikingly, F4 does acquire a capacity in transforming into a helical conformation in membrane environments. Here, for the first time, our study deciphers that like ALScausing mutants, the disruption of a well-folded E. coli cytosolic protein also unlocks its amphiphilic/hydrophobic regions which are capable of abnormally interacting with membranes. Therefore, proteins, the most important functional players for all forms of life, can transform into membrane-toxic forms triggering diseases and aging, if their hydrophobic/amphiphilic regions are unlocked by genetic, pathological or/and environmental factors, which is characteristic of severe aggregation.

Biophysics↗

bioRxiv2016

Mechanisms of self-assembly and fibrillization of the prion-like domains

The mechanism of the self-assembly and fibrillization of the prion-like domains lies at the heart of their physiology and pathology. Here with the same methods previously established, we aimed to further decipher the mechanism by characterizing two prion-like sequences with the electrostatic properties very different from that of the full-length TDP-43 prion-like domain with a very basic pI value: namely the C-half of the TDP-43 prion-like domain only abundant in Gly, Ser, Asn and Gln with a pI of ~6.3, and the FUS prion-like domain enriched with Gly, Ser, Gln and Tyr with a pI of ~3.5. Interestingly, the C-half with the TDP-43 unique hydrophobic region removed is no longer able to form insoluble aggregates/fibrils but still capable of self-assembling into the reversible hydrogel with cross-{beta} structures, despite being much slower than the full-length. On the other hand, the FUS prion-like domain rapidly self-assembles into the reversible hydrogel with cross-{beta} fibrillar structures in 1 mM phosphate buffer at pH 6.8 but its self-assembly becomes very slow in 50 mM MES buffer at pH 5.5. Our study reveals that despite having completely different electrostatic properties, the full-length and C-half of the TDP-43 prion-like domain, as well as FUS prion-like domain all have the similar pH-dependence in self-assembly as we previously reported (Lim et al., [2016] PLOS Biol 14:e1002338). This unambiguously indicates that the self-assembly of the prion-like domains is not generally governed by the electrostatic interaction. Rather, their self-assembly and fibrillization are specified by the sequences despite being highly polar and degenerative. Furthermore, our study provides the first evidence that the formation of reversible hydrogel with cross-{beta} structures is separable from fibrillization of the prion-like domain. Finally, our results also successfully reconcile the previous discrepancy about the conformation and mechanism of the self-assembly of the FUS prion-like domain.

Biophysics↗

bioRxiv2015

A novel SOD1-dependent mechanism for the iron-induced production of toxic SOD1 and oxidative stress that initiates ALS

Free iron is highly toxic and the blood-derived iron initiates early motor-neuron degeneration upon breakdown of blood-spinal cord barrier. Iron is currently known to trigger oxidative stress by Fenton chemistry but no report implies that iron manifests its toxicity through CuZn-superoxide dismutase (SOD1), the central antioxidant enzyme in all human tissues that carries >180 ALS-causing mutations. Here, by NMR we show that Zn2+ play an irreplaceable role in the maturation of the nascent hSOD1, and further decipher for the first time that out of 11 other cations only Fe2+ has the Zn2+-like capacity to induce folding to form the Fe2+-bound hSOD1. This acts to reduce or even block the maturation of wild-type and ALS-causing mutant hSOD1, consequently trapping SOD1 in toxic forms and provoking oxidative stress. Our study establishes a novel SOD1-dependent mechanism for iron to manifest cellular toxicity that contributes to pathogenesis of neurodegenerative diseases, aging and even more.\n\nOne Sentence SummaryOur study establishes a novel SOD1-dependent mechanism for iron to manifest toxicity contributing to neurodegenerative diseases, aging and even more.

Biochemistry↗