Genomes and Genes
Summary: The accumulation of an electric charge on a object
- Sheng Y, Sali A, Herzog H, Lahnstein J, Krilis S. Site-directed mutagenesis of recombinant human beta 2-glycoprotein I identifies a cluster of lysine residues that are critical for phospholipid binding and anti-cardiolipin antibody activity. J Immunol. 1996;157:3744-51 pubmed..These results indicate that the residues Lys284, Lys286, and Lys287 in the fifth domain of beta2GPI are critical for its binding to anionic phospholipids and its subsequent capture for binding of anti-beta2GPI Abs. ..
- Mathew B, Nagaraj R. Variations in the interaction of human defensins with Escherichia coli: Possible implications in bacterial killing. PLoS ONE. 2017;12:e0175858 pubmed publisher..coli is observed. Our data indicate that mammalian defensins do not kill E. coli by a simple mechanism involving membrane permeabilization though their antibacterial potencies are very similar...
- Hsu H, Hsu Y, Chang L, Yang J. An integrated approach with new strategies for QSAR models and lead optimization. BMC Genomics. 2017;18:104 pubmed publisher..These results show that our methods and new strategies can yield stable and high accuracy QSAR models. We believe that our methods and strategies are useful for discovering new leads and guiding lead optimization in drug discovery. ..
- Qiao X, Liu Y, Luo L, Chen L, Zhao C, Ai X. Effects of naturally occurring charged mutations on the structure, stability, and binding of the Pin1 WW domain. Biochem Biophys Res Commun. 2017;487:470-476 pubmed publisher..Considering that the WW domain participates in the catalytic activity of the Pin1 isomerase, our study represents a novel approach for studying Pin1 function through the analysis of its naturally occurring mutants. ..
- Lee L, Brunk N, Haywood D, Keifer D, Pierson E, Kondylis P, et al. A molecular breadboard: Removal and replacement of subunits in a hepatitis B virus capsid. Protein Sci. 2017;26:2170-2180 pubmed publisher..To test a molecular breadboard concept, we showed that missing subunits could be refilled resulting in chimeric, 120 subunit particles. This result may be a means of assembling unique capsids with functional decorations. ..
- Van Lehn R, Alexander Katz A. Free energy change for insertion of charged, monolayer-protected nanoparticles into lipid bilayers. Soft Matter. 2014;10:648-58 pubmed..This work provides physical insight that may be used to both understand the insertion of AuNPs into bilayers and guide the design of monolayers to either encourage or inhibit insertion. ..
- Rudenko A, Inhester L, Hanasaki K, Li X, Robatjazi S, Erk B, et al. Femtosecond response of polyatomic molecules to ultra-intense hard X-rays. Nature. 2017;546:129-132 pubmed publisher..Our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible. ..
- Ion B, Wells M, Chen Q, Xu Y, Tang P. Ketamine Inhibition of the Pentameric Ligand-Gated Ion Channel GLIC. Biophys J. 2017;113:605-612 pubmed publisher..Both signaling pathways have been predicted previously using the perturbation-based Markovian transmission model. The study provides a structural and dynamics basis for the inhibitory modulation of ketamine on pLGICs. ..
- Ficici E, Jeong D, Andricioaei I. Electric-Field-Induced Protein Translocation via a Conformational Transition in SecDF: An MD Study. Biophys J. 2017;112:2520-2528 pubmed publisher..Our results show that the interaction of the P1 domain dipole moment with the TM electrical field considerably lowers the free-energy barrier in the direction of F-form to I-form transition. ..
- Lee X, Verma C, Sim A. Designing dual inhibitors of Mdm2/MdmX: Unexpected coupling of water with gatekeeper Y100/99. Proteins. 2017;85:1493-1506 pubmed publisher..The recently developed potent dual inhibitory stapled peptide Atsp7041 appears to be agnostic to the conformation of the gatekeeper residue. Proteins 2017; 85:1493-1506. © 2017 Wiley Periodicals, Inc. ..
- Monteiro L, Lobenberg R, Cotrim P, Barros de Araujo G, Bou Chacra N. Buparvaquone Nanostructured Lipid Carrier: Development of an Affordable Delivery System for the Treatment of Leishmaniases. Biomed Res Int. 2017;2017:9781603 pubmed publisher..Therefore, these drug delivery systems have the potential to improve the availability of affordable medicines due to the low cost of raw materials, using well established, reliable, and feasible scale-up technology. ..
- Ross M, Fidai I, Cowan J. Analysis of Structure-Activity Relationships Based on the Hepatitis?C Virus SLIIb Internal Ribosomal Entry Sequence RNA-Targeting GGHYRFK?Cu Complex. Chembiochem. 2017;18:1743-1754 pubmed publisher..Together, the data yielded insights into structure-function relationships that will guide future optimization efforts. ..
- Kaufmann T, Grishkovskaya I, Polyansky A, Kostrhon S, Kukolj E, Olek K, et al. A novel non-canonical PIP-box mediates PARG interaction with PCNA. Nucleic Acids Res. 2017;45:9741-9759 pubmed publisher..Our data explain the mechanism of PARG-PCNA interaction through a new PARG PIP-box that exhibits non-canonical sequence properties but a canonical mode of PCNA binding. ..
- Ge J, Huang F, Nesmelov Y. Metal cation controls phosphate release in the myosin ATPase. Protein Sci. 2017;26:2181-2186 pubmed publisher..01 nm further away from ADP than in the magnesium complex. We conclude that the ionic potential of the metal cation plays a role in the retention of the abstracted phosphate. ..
- Bzymek K, Ma Y, Avery K, Horne D, Williams J. Meditope-Fab interaction: threading the hole. Acta Crystallogr F Struct Biol Commun. 2017;73:688-694 pubmed publisher..Taken together, these studies provide a basis for the design of additional modifications to enhance the overall affinity of this unique interaction...
- Mahata P, Das S. Generation of wavy structure on lipid membrane by peripheral proteins: a linear elastic analysis. FEBS Lett. 2017;591:1333-1348 pubmed publisher..It is observed that electrostatic interaction is essential for curvature generation by the BAR domains. ..
- Nagao R, Suzuki T, Dohmae N, Shen J, Tomo T. Functional role of Lys residues of Psb31 in electrostatic interactions with diatom photosystem II. FEBS Lett. 2017;591:3259-3264 pubmed publisher..These results provide evidence that some Lys residues of Psb31 are responsible for electrostatic interactions with PSII. ..
- Wang J. Experimental charge density from electron microscopic maps. Protein Sci. 2017;26:1619-1626 pubmed publisher..In principle, it should be possible to determine the charges carried by the individual atoms in macromolecules by comparing experimental CD maps with experimental ESP maps. ..
- Ribitsch D, Hromic A, Zitzenbacher S, Zartl B, Gamerith C, Pellis A, et al. Small cause, large effect: Structural characterization of cutinases from Thermobifida cellulosilytica. Biotechnol Bioeng. 2017;114:2481-2488 pubmed publisher..Biotechnol. Bioeng. 2017;114: 2481-2488. © 2017 Wiley Periodicals, Inc. ..
- Kumar S, Tsai C, Ma B, Nussinov R. Contribution of salt bridges toward protein thermostability. J Biomol Struct Dyn. 2000;17 Suppl 1:79-85 pubmed..Formation of salt bridge networks may help in explaining the increased occurrence and stability of salt bridges in hyperthermophiles. ..
- Atanasov B, Mustafi D, Makinen M. Protonation of the beta-lactam nitrogen is the trigger event in the catalytic action of class A beta-lactamases. Proc Natl Acad Sci U S A. 2000;97:3160-5 pubmed..Stabilization of ion pairs in the active site through interactions with distant clusters of charged residues in the enzyme was concluded to be an important driving force of the catalytic mechanism. ..
- Akbal Delibas B, Haspel N. A conservation and biophysics guided stochastic approach to refining docked multimeric proteins. BMC Struct Biol. 2013;13 Suppl 1:S7 pubmed publisher..We aim to incorporate our refinement method in a larger framework which also enables docking of multimeric complexes given only monomeric structures. ..
- Chow E, Skolnick J. DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid. Biophys J. 2017;112:2261-2270 pubmed publisher..The internal motions of DNA appear to be governed by strong internal forces arising from being crowded into the small space of the nucleoid. A consequence of the DNA internal motion is that protein target search may be accelerated. ..
- Huang Y, Gao M, Yang F, Zhang L, Su Z. Deciphering the promiscuous interactions between intrinsically disordered transactivation domains and the KIX domain. Proteins. 2017;85:2088-2095 pubmed publisher..This study highlights the importance of long-range electrostatic interactions in molecular recognition process involving multi-motif intrinsically disordered proteins and promiscuous interactions. ..
- Chandra B, Bhowmik D, Maity B, Mote K, Dhara D, Venkatramani R, et al. Major Reaction Coordinates Linking Transient Amyloid-? Oligomers to Fibrils Measured at Atomic Level. Biophys J. 2017;113:805-816 pubmed publisher..Overall, we propose interstrand separation and salt-bridge formation as key reaction coordinates describing the structural transition of the small A?40 oligomers to fibrils. ..
- Azimzadeh Irani M, Kannan S, Verma C. Role of N-glycosylation in EGFR ectodomain ligand binding. Proteins. 2017;85:1529-1549 pubmed publisher..Analysis of SNP data suggests the possibility of altered glycosylation with functional consequences. Proteins 2017; 85:1529-1549. © 2017 Wiley Periodicals, Inc. ..
- Amara C, Degraeve P, Oulahal N, Gharsallaoui A. pH-dependent complexation of lysozyme with low methoxyl (LM) pectin. Food Chem. 2017;236:127-133 pubmed publisher..The role of electrostatic interactions in the formation of lysozyme/LM pectin complexes is discussed in relation to the overall structure and the charge density profile of the two biopolymers. ..
- Temprana C, Prieto M, Igartúa D, Femia A, Amor M, Alonso S. Diacetylenic lipids in the design of stable lipopolymers able to complex and protect plasmid DNA. PLoS ONE. 2017;12:e0186194 pubmed publisher..Thus, this work represents the first steps toward developing a cationic lipopolymer-based gene delivery system using polymerizable and cationic lipids...
- Pulsipher K, Villegas J, Roose B, Hicks T, Yoon J, Saven J, et al. Thermophilic Ferritin 24mer Assembly and Nanoparticle Encapsulation Modulated by Interdimer Electrostatic Repulsion. Biochemistry. 2017;56:3596-3606 pubmed publisher..This work illustrates designed protein cages with distinct assembly and encapsulation properties. ..
- Lolli G, Naressi D, Sarno S, Battistutta R. Characterization of the oligomeric states of the CK2 ?2?2 holoenzyme in solution. Biochem J. 2017;474:2405-2416 pubmed publisher..A significant novel finding is that a considerable amount of monomer, the active form of CK2, is present also at low salt. The solution properties of CK2 shown in the present study complement the model of regulation by polymerization. ..
- Nomura M, Aiamla Or S, Tanaka S, Shigyo M, Masuda Y, Yamauchi N. Effect of reactive oxygen species on quality maintenance of broccoli florets with electrostatic atomized water particle treatment. Food Chem. 2017;237:749-755 pubmed publisher..These findings suggested that hydrogen peroxide formed by EAWP treatment and regulated by CAT could be relevant to maintaining the quality of broccoli. ..
- Nagao R, Suzuki T, Okumura A, Kihira T, Toda A, Dohmae N, et al. Electrostatic interaction of positive charges on the surface of Psb31 with photosystem II in the diatom Chaetoceros gracilis. Biochim Biophys Acta Bioenerg. 2017;1858:779-785 pubmed publisher..Based on these findings, together with our previous cross-linking study in diatom PSII and a red algal PSII structure, we discuss binding properties of Psb31 with PSII core proteins. ..
- Lee J, Suárez González D, Murphy W. Mineral coatings for temporally controlled delivery of multiple proteins. Adv Mater. 2011;23:4279-84 pubmed
- Terauchi Y, Kim Y, Tanaka T, Nanatani K, Takahashi T, Abe K. Asp30 of Aspergillus oryzae cutinase CutL1 is involved in the ionic interaction with fungal hydrophobin RolA. Biosci Biotechnol Biochem. 2017;81:1363-1368 pubmed publisher..Our results indicate that D30 is a novel residue involved in the ionic interaction between RolA and CutL1. ..
- Yau W, Wimley W, Gawrisch K, White S. The preference of tryptophan for membrane interfaces. Biochemistry. 1998;37:14713-8 pubmed
- Kriegel F, Ermann N, Forbes R, Dulin D, Dekker N, Lipfert J. Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers. Nucleic Acids Res. 2017;45:5920-5929 pubmed publisher..5 pN) torsional stiffness values of C = 103 ± 4 nm are identical, within experimental errors, for all tested salt concentration, suggesting that the intrinsic torsional stiffness of DNA does not depend on salt. ..
- Vineeth Kumar T, Sanil G. A Review of the Mechanism of Action of Amphibian Antimicrobial Peptides Focusing on Peptide-Membrane Interaction and Membrane Curvature. Curr Protein Pept Sci. 2017;18:1263-1272 pubmed publisher..In addition, the models proposed to explain the mechanism of action of membrane lytic and non-lytic AMPs are also reviewed. ..
- Creagh A, Ong E, Jervis E, Kilburn D, Haynes C. Binding of the cellulose-binding domain of exoglucanase Cex from Cellulomonas fimi to insoluble microcrystalline cellulose is entropically driven. Proc Natl Acad Sci U S A. 1996;93:12229-34 pubmed..Differential heat capacity changes are large and negative, indicating that sorbent and protein dehydration effects make a dominant contribution to the driving force for binding. ..
- Yang F, Jiang Q, Xie W, Zhang Y. Effects of multi-walled carbon nanotubes with various diameters on bacterial cellular membranes: Cytotoxicity and adaptive mechanisms. Chemosphere. 2017;185:162-170 pubmed publisher..subtilis, indicating that electrostatic repulsion between the material and bacteria leading to the decrease of direct contact may be the primary factor that reduces the impacts from MWNTs. ..
- Plumridge A, Meisburger S, Andresen K, Pollack L. The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res. 2017;45:3932-3943 pubmed publisher..These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these systems. ..
- Rosú S, Toledo L, Urbano B, Sanchez S, Calabrese G, Tricerri M. Learning from Synthetic Models of Extracellular Matrix; Differential Binding of Wild Type and Amyloidogenic Human Apolipoprotein A-I to Hydrogels Formed from Molecules Having Charges Similar to Those Found in Natural GAGs. Protein J. 2017;36:374-383 pubmed publisher..These results show the importance of the use of these polymers as a model to get deep insight into the studies of proteins within macromolecules. ..
- Nguyen H, Oguchi H, Van Minh L, Kuwano H. High-Throughput Investigation of a Lead-Free AlN-Based Piezoelectric Material, (Mg,Hf)xAl1-xN. ACS Comb Sci. 2017;19:365-369 pubmed publisher..These results verified that (Mg,Hf)xAl1-xN is a promising material for piezoelectric-based application devices, especially for vibrational energy harvesters...
- Rossano R, Larocca M, Riviello L, Coniglio M, Vandooren J, Liuzzi G, et al. Heterogeneity of serum gelatinases MMP-2 and MMP-9 isoforms and charge variants. J Cell Mol Med. 2014;18:242-52 pubmed..These observations open perspectives for better diagnosis and prognosis of many diseases and need to be critically interpreted when applying other methods for MS and other diseases. ..
- Ibarra Molero B, Loladze V, Makhatadze G, Sanchez Ruiz J. Thermal versus guanidine-induced unfolding of ubiquitin. An analysis in terms of the contributions from charge-charge interactions to protein stability. Biochemistry. 1999;38:8138-49 pubmed..In general, our analysis suggests the possibility of enhancing protein thermal stability by adequately redesigning the distribution of solvent-exposed, charged residues on the native protein surface. ..
- Gupta S, Kesarla R, Chotai N, Misra A, Omri A. Systematic Approach for the Formulation and Optimization of Solid Lipid Nanoparticles of Efavirenz by High Pressure Homogenization Using Design of Experiments for Brain Targeting and Enhanced Bioavailability. Biomed Res Int. 2017;2017:5984014 pubmed publisher
- Molt R, Georgiadis M, Richards N. Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 ?s molecular dynamics simulations. Nucleic Acids Res. 2017;45:3643-3653 pubmed publisher..Second, differences are seen in the base stacking of pairs in dinucleotide steps, arising from energetically favorable stacking of the nitro group in with ?-electrons of the adjacent base. ..
- Wu G, Li Y, Wei D, He F, Jiang S, Hu G, et al. Solution structure of BmP01 from the venom of scorpion Buthus martensii Karsch. Biochem Biophys Res Commun. 2000;276:1148-54 pubmed..Asp 20 to Lys 23 form a type II turn linking the two strands. Structural and electrostatic potential comparison between BmP01 and its analogues are also presented. ..
- Nguyen T, Nguyen T, Nguyen C, Nguyen D. Redox and pH Responsive Poly (Amidoamine) Dendrimer-Heparin Conjugates via Disulfide Linkages for Letrozole Delivery. Biomed Res Int. 2017;2017:8589212 pubmed publisher..These results demonstrated that the P-SS-Hep conjugates could be a promising candidate as redox and pH responsive nanocarriers for cancer chemotherapy. ..
- Schmidt K, Prakash T, Donner A, Kinberger G, Gaus H, Low A, et al. Characterizing the effect of GalNAc and phosphorothioate backbone on binding of antisense oligonucleotides to the asialoglycoprotein receptor. Nucleic Acids Res. 2017;45:2294-2306 pubmed publisher..Our results provide insights into how backbone charge and chemical composition assist in the binding and internalization of highly polar anionic single stranded oligonucleotides into cells and tissues. ..
- Kubli Garfias C, Vázquez Ramírez R, Trejo Muñoz C, Berber A. Insights on the mechanism of action of immunostimulants in relation to their pharmacological potency. The effects of imidazoquinolines on TLR8. PLoS ONE. 2017;12:e0178846 pubmed publisher..These findings may facilitate the development and design of improved small molecules with IMMS properties that are targeted to the TLR system and have enhanced pharmacological effectiveness and reduced toxicity. ..
- Ward J, Merritt L, Calligaro D, Bymaster F, Shannon H, Mitch C, et al. 1,2,5-Thiadiazole analogues of aceclidine as potent m1 muscarinic agonists. J Med Chem. 1998;41:379-92 pubmed..Several of these new 1,2,5-thiadiazoles have m1 agonist efficacy, potency, and selectivity comparable to those of xanomeline 2 in the muscarinic tests investigated. ..
- Kayode O, Huang Z, Soares A, Caulfield T, Dong Z, Bode A, et al. Small molecule inhibitors of mesotrypsin from a structure-based docking screen. PLoS ONE. 2017;12:e0176694 pubmed publisher..25 Å resolution. This high resolution crystal structure can now offer a foundation for structure-guided efforts to develop novel and potentially more selective mesotrypsin inhibitors based on similar molecular substructures. ..
- Yamasaki K, Daiho T, Danko S, Yasuda S, Suzuki H. Nanodisc-based kinetic assays reveal distinct effects of phospholipid headgroups on the phosphoenzyme transition of sarcoplasmic reticulum Ca2+-ATPase. J Biol Chem. 2017;292:20218-20227 pubmed publisher..Our analyses further revealed that the surface charge of the lipid bilayer directly modulates the transition rate. ..
- Srivastava A, Hardy E, Allen J, Vaccaro B, Johnson M, Knaff D. Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase. Biochemistry. 2017;56:5582-5592 pubmed publisher..The R43Q, R46Q, K201Q, and K614Q NR variants also showed a decreased binding affinity for Fd, compared to that of wild-type NR, supporting a key role of these four positively charged residues in the productive binding of Fd...
- Priya P, Maity A, Ghosh Dastidar S. The long unstructured region of Bcl-xl modulates its structural dynamics. Proteins. 2017;85:1567-1579 pubmed publisher..Proteins 2017; 85:1567-1579. © 2017 Wiley Periodicals, Inc. ..
- Yang X, Li Z, Gao Z, Wang W, Geng Z, Xu J, et al. Structural and SAXS analysis of Tle5-Tli5 complex reveals a novel inhibition mechanism of H2-T6SS in Pseudomonas aeruginosa. Protein Sci. 2017;26:2083-2091 pubmed publisher..We also distinguished the structural features of Tle5 and Tle5B family immunity proteins. Together, our work provided insights into a novel inhibition mechanism that may enhance our understanding of phospholipase D family proteins. ..
- Ozdilek B, Thompson V, Ahmed N, White C, Batey R, Schwartz J. Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding. Nucleic Acids Res. 2017;45:7984-7996 pubmed publisher..Analysis of RGG/RG domains from FUS, FMRP and hnRNPU against a spectrum of contrasting RNAs reveals that each display degenerate binding specificity, while still displaying different degrees of preference for RNA. ..
- Wang Q, Irobalieva R, Chiu W, Schmid M, Fogg J, Zechiedrich L, et al. Influence of DNA sequence on the structure of minicircles under torsional stress. Nucleic Acids Res. 2017;45:7633-7642 pubmed publisher..Our results indicate that the conformational distribution of minicircles under torsional stress can be designed, which has important implications for using minicircle DNA for gene therapy. ..
- Wilson G, Pascual J, Brooijmans N, Murray D, Karlin A. The intrinsic electrostatic potential and the intermediate ring of charge in the acetylcholine receptor channel. J Gen Physiol. 2000;115:93-106 pubmed..These electrostatic properties were simulated by theoretical calculations based on a simplified model of the channel. ..