Rxivist logo

Rxivist.org combines preprints from bioRxiv.org with data from Twitter to help you find the papers being discussed in your field.
Currently indexing 88,613 bioRxiv papers from 380,028 authors.

Most downloaded bioRxiv papers, all time

Results 1781 through 1800 out of 2848

in category biochemistry

 

1781: KLK4 inhibition by cyclic and acyclic peptides: structural and dynamical insights into standard-mechanism protease inhibitors

Blake T. Riley, Olga Ilyichova et al.

263 downloads (posted 08 Mar 2019)

Sunflower Trypsin Inhibitor (SFTI-1) is a 14-amino acid serine protease inhibitor. The dual anti-parallel β-sheet arrangement of SFTI-1 is stabilized by a N-terminal-C-terminal backbone cyclization and a further disulfide bridge to form a final bicyclic structure. This constrained structure is further rigidified by an extensive network of internal hydrogen bonds. Thus, the structure of SFTI-1 in solution resembles the protease-bound structure, reducing the entropic penalty upon protease binding. When cleaved at the scissile bond, it is thought that the rigidifying features of SFTI-1 maintain its structure, allowing the scissile bond to be reformed. The lack of structural plasticity for SFTI-1 is proposed to favour initial protease binding and continued occupancy in the protease active site, resulting in an equilibrium between cleaved and uncleaved inhibitor in the presence of protease. We have determined, at 1.15 Å resolution, the x-ray crystal structures of complexes between human kallikrein-related peptidase 4 (KLK4) and SFTI-FCQR(Asn14), and between KLK4 and an acyclic form of the same inhibitor, SFTI-FCQR(Asn14)[1,14], with the latter displaying a cleaved scissile bond. Structural analysis and MD simulations together reveal the roles of altered contact sequence, intramolecular hydrogen bonding network and backbone cyclization, in altering the state of SFTI's scissile bond ligation at the protease active site. Taken together, the data presented reveal insights into the role of dynamics in the standard-mechanism inhibition, and suggest that modifications on the non-contact strand may be a useful, underexplored approach for generating further potent or selective SFTI-based inhibitors against members of the serine protease family.

https://rxivist.org/papers/45554
https://doi.org/10.1101/570390

1782: A single K+-binding site in the crystal structure of the gastric proton pump

Kenta Yamamoto, Vikas Dubey et al.

263 downloads (posted 15 Apr 2019)

The gastric proton pump (H+,K+-ATPase), a P-type ATPase responsible for gastric acidification, mediates electro-neutral exchange of H+ and K+ coupled with ATP hydrolysis, but with an as yet undetermined transport stoichiometry. Here we show crystal structures at a resolution of 2.5 Å of the pump in the E2-P transition state, in which the counter-transporting cation is occluded. We found a single K+ bound to the cation-binding site of H+,K+-ATPase, indicating an exchange of 1H+/1K+ per hydrolysis of one ATP molecule. Thi...

https://rxivist.org/papers/48576
https://doi.org/10.1101/608851

1783: Bayogenin 3-O-Cellobioside is a novel non-cultivar specific anti-blast metabolite produced in rice in response to Pyricularia oryzae infection

Justice Norvienyeku, Lili Lin et al.

263 downloads (posted 23 May 2019)

Rice cultivars from japonica and indica lineage possess differential resistance against blast fungus on an account genetic divergence. Whether different rice cultivars also show distinct metabolomic changes in response to P. oryzae, and their role in host resistance, are poorly understood. Here, we examine the responses of six different rice cultivars from japonica and indica lineage challenged with P. oryzae. Both susceptible and resistant rice cultivars expressed several metabolites exclusively during P. oryzae infect...

https://rxivist.org/papers/51440
https://doi.org/10.1101/647636

1784: Monitoring the production of high diffraction-quality crystals of two enzymes in real time using in situ dynamic light scattering

Raphaël de Wijn, Kévin Rollet et al.

262 downloads (posted 06 Jan 2020)

The reproducible preparation of well diffracting crystals is a prerequisite for every structural study based on crystallography. An instrument called the XtalController has recently been designed that allows the monitoring of crystallization assays using dynamic light scattering and microscopy, and integrates piezo pumps to alter the composition of the mother liquor during the experiment. We have applied this technology to study the crystallization of two enzymes, the CCA-adding enzyme of the psychrophilic bacterium Pla...

https://rxivist.org/papers/70172
https://doi.org/10.1101/2020.01.05.888370

1785: Real Time Normalization of Fast Photochemical Oxidation of Proteins Experiments by Inline Adenine Radical Dosimetry

Joshua S. Sharp, Sandeep K. Misra et al.

262 downloads (posted 20 Jun 2018)

Hydroxyl radical protein footprinting (HRPF) is a powerful method for measuring protein topography, allowing researchers to monitor events that alter the solvent accessible surface of a protein (e.g. ligand binding, aggregation, conformational changes, etc.) by measuring changes in the apparent rate of reaction of portions of the protein to hydroxyl radicals diffusing in solution. Fast Photochemical Oxidation of Proteins (FPOP) offers an ultra-fast benchtop method for performing HRPF, photolyzing hydrogen peroxide using...

https://rxivist.org/papers/10845
https://doi.org/10.1101/352385

1786: Zinc(II) binding on human wild-type ISCU and Met140 variants modulates Fe-S complex activity

Nicholas G Fox, Alain Martelli et al.

262 downloads (posted 10 Feb 2018)

The human de novo iron-sulfur (Fe-S) assembly complex consists of the cysteine desulfurase NFS1, accessory protein ISD11, scaffold protein ISCU, and allosteric activator frataxin (FXN). FXN has been shown to bind the NFS1-ISD11-ISCU complex (SDU), to activate the desulfurase activity and thus Fe-S cluster biosynthesis. Conversely, in the absence of FXN, the NFS1-ISD11 (SD) complex was reported to be inhibited by the binding of recombinant ISCU. Here, we show that recombinant ISCU binds zinc(II) ion, and that the presenc...

https://rxivist.org/papers/11059
https://doi.org/10.1101/262477

1787: A model-free method for measuring dimerization free energies of CLC-ec1 in lipid bilayers

Rahul Chadda, Lucy Cliff et al.

262 downloads (posted 23 Jun 2017)

We previously reported the equilibrium dimerization reaction of the CLC-ec1 Cl-/H+ transporter in 2:1 POPE/POPG membranes (Chadda et al. 2016). This was determined by measuring the probability distributions of subunit capture into extruded liposomes by single-molecule photobleaching analysis across a wide range of subunit/lipid mole fraction densities. In this approach, knowledge of the liposome size distribution is necessary in order to correct the data for random co-capture events and extract the underlying dimerizati...

https://rxivist.org/papers/11302
https://doi.org/10.1101/154286

1788: The Ras-like GTPase Rem2 is a potent endogenous inhibitor of calcium/calmodulin-dependent kinase II activity

Leandro Royer, Josiah J. Herzog et al.

262 downloads (posted 12 Jun 2017)

CaMKII is a well-characterized, abundant protein kinase that regulates a diverse set of functions in a tissue specific manner. For example, in heart muscle, CaMKII regulates Ca2+ homeostasis while in neurons CaMKII regulates activity-dependent dendritic remodeling and Long Term Potentiation (LTP), a biological correlate of learning and memory. Previously, we identified the noncanonical GTPase Rem2 as a critical regulator of dendrite branching and synapse formation in the vertebrate nervous system. Here, we report that R...

https://rxivist.org/papers/11321
https://doi.org/10.1101/148981

1789: Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics

Yinglong Miao, Apurba Bhattarai et al.

262 downloads (posted 21 Apr 2020)

Calculations of ligand binding free energies and kinetic rates are important for drug design. However, such tasks have proven challenging in computational chemistry and biophysics. To address this challenge, we have developed a new computational method "LiGaMD", which selectively boosts the ligand non-bonded interaction potential energy based on the Gaussian accelerated molecular dynamics (GaMD) enhanced sampling technique. Another boost potential could be applied to the remaining potential energy of the entire system i...

https://rxivist.org/papers/80586
https://doi.org/10.1101/2020.04.20.051979

1790: The E3 ubiquitin ligase Pib1 regulates effective gluconeogenic shutdown in S. cerevisiae.

Vineeth Vengayil, Sunil Laxman

262 downloads (posted 17 Jun 2019)

Cells use multiple mechanisms to regulate their metabolic states depending on changes in their nutrient environment. A well-known example is the response of cells to glucose availability. In S. cerevisiae cells growing in glucose-limited medium, the re-availability of glucose leads to the downregulation of gluconeogenesis, the activation of glycolysis, and robust glucose repression. However, our knowledge of the initial mechanisms mediating this glucose-dependent downregulation of the gluconeogenic transcription factors...

https://rxivist.org/papers/53495
https://doi.org/10.1101/673657

1791: Elucidating the roles of Alzheimer disease-associated proteases and the signal-peptide peptidase-like 3 (SPPL3) in the shedding of glycosyltransferases

Assou El-Battari, Sylvie Mathieu et al.

261 downloads (posted 08 May 2018)

The Golgi resident glycosyltransferases (GTs) are membrane-bound glycoproteins but are frequently found as soluble proteins in biological fluids where their function remains largely unknown. Previous studies have established that the release of these proteins involved Alzheimer disease-associated proteases such as β-secretases (BACE1 and BACE2) and the intramembrane-cleaving aspartyl proteases Presenilins 1 and 2. Recent studies have involved another intramembrane-cleaving enzyme, the signal peptide peptidese-like-3 (SP...

https://rxivist.org/papers/10942
https://doi.org/10.1101/317214

1792: A DNA G-quadruplex/i-motif hybrid

Betty Chu, Daoning Zhang et al.

261 downloads (posted 15 Aug 2019)

DNA can form many structures beyond the canonical Watson-Crick double helix. It is now clear that noncanonical structures are present in genomic DNA and have biological functions. G-rich G-quadruplexes and C-rich i-motifs are the most well-characterized noncanonical DNA motifs that have been detected in vivo with either proscribed or postulated biological roles. Because of their independent sequence requirements, these structures have largely been considered distinct types of quadruplexes. Here, we describe the crystal ...

https://rxivist.org/papers/58325
https://doi.org/10.1101/737296

1793: A conserved D/E-P motif in the nucleotide binding domain of plant ABCB/PGP-type ABC transporters defines their auxin transport capacity

Pengchao Hao, Jian Xia et al.

261 downloads (posted 09 May 2020)

Auxin transport activity of ABCB1 was suggested to be regulated by physical interaction with the FKBP42/Twisted Dwarf1 (TWD1), a bona fide peptidylprolyl cis-trans isomerase (PPIase), but all attempts to demonstrate such a PPIase activity on TWD1 have failed so far. By using a structure-based approach we have identified a series of surface-exposed proline residues in the C- terminal nucleotide binding fold and linker of Arabidopsis ABCB1 that do not alter ABCB1 protein stability or location but its catalytic transport a...

https://rxivist.org/papers/82812
https://doi.org/10.1101/2020.05.08.084087

1794: Molecular Architecture of the Bardet-Biedl Syndrome Protein 2-7-9 Subcomplex

W. Grant Ludlam, Takuma Aoba et al.

261 downloads (posted 11 Jul 2019)

Bardet-Biedl syndrome (BBS) is a genetic disease caused by mutations that disrupt the function of the BBSome, an eight-subunit complex that plays an important role in transport of proteins in primary cilia. To better understand the molecular basis of the disease, we analyzed the structure of a BBSome subcomplex consisting of three homologous BBS proteins (BBS2, BBS7, and BBS9) by an integrative structural modeling approach using electron microscopy and chemical crosslinking coupled with mass spectrometry. The resulting ...

https://rxivist.org/papers/55518
https://doi.org/10.1101/699223

1795: Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements

Rory Henderson, Maolin Lu et al.

261 downloads (posted 02 Nov 2019)

The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced exposure of the co-receptor binding site and fusion elements. To understand the molecular details of this allostery, we introduced Env mutations aimed to prevent CD4-induced rearrangements in the HIV-1 BG505 Env trimer. Binding analysis performed on the soluble ectodomain BG505 SOSIP Env trimers, cell-surface expressed BG505 f...

https://rxivist.org/papers/65239
https://doi.org/10.1101/827857

1796: Dextranol: A better lyoprotectant

Bryan J Jones, Advitiya Mahajan et al.

260 downloads (posted 07 Dec 2018)

Dextranol, a reduced dextran, prevents damage to stored dry protein samples that unmodified dextran would otherwise cause. Lyoprotectants like the polysaccharide dextran are critical for preserving dried protein samples by forming rigid a glass that protects entrapped protein molecules. Stably dried proteins are important for maintaining critical information in clinical samples like blood serum. However, we found that dextran reacts with serum proteins during storage, producing high-molecular weight Amadori-product conj...

https://rxivist.org/papers/38459
https://doi.org/10.1101/490441

1797: Dscam homophilic specificity is generated by high order cis-multimers coupled with trans self-binding of variable Ig1 in Chelicerata

Fengyan Zhou, Guozheng Cao et al.

260 downloads (posted 16 Dec 2019)

By alternative splicing, Drosophila Down syndrome cell adhesion molecule (Dscam1) encodes tens of thousands of proteins required for establishing neural circuits, while Chelicerata encodes a family of ~ 100 shortened Dscam (sDscam) isoforms via alternative promoters. We report that Dscam isoforms interact promiscuously in cis to generate a vast repertoire of combinatorial homophilic recognition specificities in Chelicerata. Specifically, sDscams formed high order cis-multimers without isoform specificity involving the m...

https://rxivist.org/papers/68870
https://doi.org/10.1101/2019.12.15.877159

1798: The Hrq1 helicase stimulates Pso2 translesion nuclease activity to promote DNA inter-strand crosslink repair

Cody M. Rogers, Chun-Ying Lee et al.

260 downloads (posted 18 Sep 2019)

DNA inter-strand crosslink (ICL) repair requires a complicated network of DNA damage response pathways. Removal of these lesions is vital as they are physical barriers to essential DNA processes that require the separation of duplex DNA, such as replication and transcription. The Fanconi anemia (FA) pathway is the principle mechanism for ICL repair in metazoans and is coupled to replication. In Saccharomyces cerevisiae , a degenerate FA pathway is present, but ICLs are predominantly repaired by a pathway involving the P...

https://rxivist.org/papers/61009
https://doi.org/10.1101/773267

1799: A proteome-based design of bitter peptide digestion regime to attenuate cod-bone soup bitterness: comparison with a rainbow trout extract-mediated bitter taste masking approach

Ying Han, Changlu Guo et al.

260 downloads (posted 21 Mar 2018)

BACKGROUND: The fresh bones (with some meat on them; frequently discarded as a large quantity of industry garbage) of marine fish such as cod and salmon are good materials for manufacture of food additives (taste adjusters). However, such fish-bone originated additives often have apparent bitter taste and need additional debittering regime. RESULTS: In this study, 46 known bitter peptides in the cod proteome were targeted for specific protease digestion to eliminate bitter taste from the cod bone soup. Though the debitt...

https://rxivist.org/papers/11021
https://doi.org/10.1101/279265

1800: Interaction of NPC2 protein with Lysobisphosphatidic Acid is required for normal endolysosomal cholesterol trafficking

Leslie A McCauliff, Annette Langan et al.

260 downloads (posted 24 Feb 2019)

Unesterified cholesterol accumulation in the late endosomal/lysosomal (LE/LY) compartment is the cellular hallmark of Niemann-Pick C (NPC) disease, caused by defects in the genes encoding NPC1 or NPC2. We previously reported the dramatic stimulation of NPC2 cholesterol transport rates by the LE/LY phospholipid lysobisphosphatidic acid (LBPA) and in these studies sought to determine their functional relationship in normal LE/LY cholesterol egress. Here we demonstrate that NPC2 interacts directly with LBPA and identify th...

https://rxivist.org/papers/44688
https://doi.org/10.1101/559849