College of Liberal Arts & Sciences
Subscribe to Recent Comp Bio Pubs feed Recent Comp Bio Pubs
NCBI: db=pubmed; Term=(Im, Wonpil[Author] AND Kansas) OR (Vakser, Ilya[Author]) OR (Karanicolas, John[Author] AND Kansas) OR (Deeds, Eric[Author]) OR (Ray, Christian[Author]) OR (Slusky, Joanna[Author]) OR (Ray JC[Author] AND Kansas)
Updated: 3 hours 8 min ago

Asymmetric Cryo-EM Structure of Anthrax Toxin Protective Antigen Pore with Lethal Factor N-Terminal Domain.

Sat, 09/23/2017 - 10:03

Asymmetric Cryo-EM Structure of Anthrax Toxin Protective Antigen Pore with Lethal Factor N-Terminal Domain.

Toxins (Basel). 2017 Sep 22;9(10):

Authors: Machen AJ, Akkaladevi N, Trecazzi C, O'Neil PT, Mukherjee S, Qi Y, Dillard R, Im W, Gogol EP, White TA, Fisher MT

Abstract
The anthrax lethal toxin consists of protective antigen (PA) and lethal factor (LF). Understanding both the PA pore formation and LF translocation through the PA pore is crucial to mitigating and perhaps preventing anthrax disease. To better understand the interactions of the LF-PA engagement complex, the structure of the LFN-bound PA pore solubilized by a lipid nanodisc was examined using cryo-EM. CryoSPARC was used to rapidly sort particle populations of a heterogeneous sample preparation without imposing symmetry, resulting in a refined 17 Å PA pore structure with 3 LFN bound. At pH 7.5, the contributions from the three unstructured LFN lysine-rich tail regions do not occlude the Phe clamp opening. The open Phe clamp suggests that, in this translocation-compromised pH environment, the lysine-rich tails remain flexible and do not interact with the pore lumen region.

PMID: 28937604 [PubMed - in process]

Modeling CAPRI Targets 110 - 120 by Template-Based and Free Docking Using Contact Potential and Combined Scoring Function.

Fri, 09/15/2017 - 16:08
Related Articles

Modeling CAPRI Targets 110 - 120 by Template-Based and Free Docking Using Contact Potential and Combined Scoring Function.

Proteins. 2017 Sep 14;:

Authors: Kundrotas PJ, Anishchenko I, Badal VD, Das M, Dauzhenka T, Vakser IA

Abstract
The paper presents analysis of our template-based and free docking predictions in the joint CASP12/CAPRI37 round. A new scoring function for template-based docking was developed, benchmarked on the Dockground resource, and applied to the targets. The results showed that the function successfully discriminates the incorrect docking predictions. In correctly predicted targets, the scoring function was complemented by other considerations, such as consistency of the oligomeric states among templates, similarity of the biological functions, biological interface relevance, etc. The scoring function still does not distinguish well biological from crystal packing interfaces, and needs further development for the docking of bundles of α-helices. In the case of the trimeric targets, sequence-based methods did not find common templates, despite similarity of the structures, suggesting complementary use of structure- and sequence-based alignments in comparative docking. The results showed that if a good docking template is found, an accurate model of the interface can be built even from largely inaccurate models of individual subunits. Free docking however is very sensitive to the quality of the individual models. However, our newly developed contact potential detected approximate locations of the binding sites. This article is protected by copyright. All rights reserved.

PMID: 28905425 [PubMed - as supplied by publisher]

Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores.

Wed, 09/13/2017 - 15:09
Related Articles

Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores.

Proteins. 2015 Dec;83(12):2293-306

Authors: Parente DJ, Ray JC, Swint-Kruse L

Abstract
As proteins evolve, amino acid positions key to protein structure or function are subject to mutational constraints. These positions can be detected by analyzing sequence families for amino acid conservation or for coevolution between pairs of positions. Coevolutionary scores are usually rank-ordered and thresholded to reveal the top pairwise scores, but they also can be treated as weighted networks. Here, we used network analyses to bypass a major complication of coevolution studies: For a given sequence alignment, alternative algorithms usually identify different, top pairwise scores. We reconciled results from five commonly-used, mathematically divergent algorithms (ELSC, McBASC, OMES, SCA, and ZNMI), using the LacI/GalR and 1,6-bisphosphate aldolase protein families as models. Calculations used unthresholded coevolution scores from which column-specific properties such as sequence entropy and random noise were subtracted; "central" positions were identified by calculating various network centrality scores. When compared among algorithms, network centrality methods, particularly eigenvector centrality, showed markedly better agreement than comparisons of the top pairwise scores. Positions with large centrality scores occurred at key structural locations and/or were functionally sensitive to mutations. Further, the top central positions often differed from those with top pairwise coevolution scores: instead of a few strong scores, central positions often had multiple, moderate scores. We conclude that eigenvector centrality calculations reveal a robust evolutionary pattern of constraints-detectable by divergent algorithms--that occur at key protein locations. Finally, we discuss the fact that multiple patterns coexist in evolutionary data that, together, give rise to emergent protein functions.

PMID: 26503808 [PubMed - indexed for MEDLINE]

Dockground: A comprehensive data resource for modeling of protein complexes.

Tue, 09/12/2017 - 14:10
Related Articles

Dockground: A comprehensive data resource for modeling of protein complexes.

Protein Sci. 2017 Sep 10;:

Authors: Kundrotas PJ, Anishchenko I, Dauzhenka T, Kotthoff I, Mnevets D, Copeland MM, Vakser IA

Abstract
Characterization of life processes at the molecular level requires structural details of protein interactions. The number of experimentally determined structures of protein-protein complexes accounts only for a fraction of known protein interactions. This gap in structural description of the interactome has to be bridged by modeling. An essential part of the development of structural modeling/docking techniques for protein interactions is databases of protein-protein complexes. They are necessary for studying protein interfaces, providing a knowledge base for docking algorithms, developing intermolecular potentials, search procedures, and scoring functions. Development of protein-protein docking techniques requires thorough benchmarking of different parts of the docking protocols on carefully curated sets of protein-protein complexes. We present a comprehensive description of the Dockground resource (http://dockground.compbio.ku.edu) for structural modeling of protein interactions, including previously unpublished unbound docking benchmark set 4, and the X-ray docking decoy set 2. The resource offers a variety of interconnected datasets of protein-protein complexes and other data for the development and testing of different aspects of protein docking methodologies. Based on protein-protein complexes extracted from the PDB biounit files, Dockground offers sets of X-ray unbound, simulated unbound, model, and docking decoy structures. All datasets are freely available for download, as a whole or selecting specific structures, through a user-friendly interface on one integrated website. This article is protected by copyright. All rights reserved.

PMID: 28891124 [PubMed - as supplied by publisher]

Identification of novel small molecule Beclin 1 mimetics activating autophagy.

Sat, 09/09/2017 - 13:03
Related Articles

Identification of novel small molecule Beclin 1 mimetics activating autophagy.

Oncotarget. 2017 Aug 01;8(31):51355-51369

Authors: Yu J, Lan L, Lewin SJ, Rogers SA, Roy A, Wu X, Gao P, Karanicolas J, Aubé J, Sun B, Xu L

Abstract
Anti-apoptotic proteins Bcl-2 and Bcl-xL could block autophagy by binding to Beclin 1 protein, an essential inducer of autophagy. Compounds mimicking Beclin 1 might be able to disrupt Bcl-xL/2-Beclin 1 interaction, free out Beclin 1, and thus trigger autophagy. In order to identify small molecule Beclin 1 mimetics, a fluorescence polarization-based high-throughput screening of 50,316 compounds was carried out with a Z' score of 0.82 ± 0.05, and an outcome of 58 hits. After the structure analysis, three acridine analogues were unveiled and confirmed using the fluorescence polarization assay and the surface plasmon resonance assay. Moreover, a set of 17 additional acridine analogues was prepared and tested. Compound 7 showed selectivity for Bcl-xL (KD = 6.5 μM) over Bcl-2 (KD = 160 μM) protein, and potent cytotoxicity (nanomolar scale) in PC-3, PC-3a and DU145 prostate cancer cells. Furthermore, induction of autophagy was also demonstrated in PC-3 and PC-3a cells treated with some acridine compounds by LC3 conversion immunoblotting and LC3 fluorescence microscopy. These Beclin 1 mimetics will be invaluable tools for developing novel autophagy inducers, better understanding the roles of autophagy in cancer, and will contribute to cancer therapy.

PMID: 28881653 [PubMed - in process]

Comparative Characterization of Crofelemer Samples using Data Mining and Machine Learning Approaches with Analytical Stability Data Sets.

Thu, 07/27/2017 - 13:13
Related Articles

Comparative Characterization of Crofelemer Samples using Data Mining and Machine Learning Approaches with Analytical Stability Data Sets.

J Pharm Sci. 2017 Jul 22;:

Authors: Nariya MK, Kim JH, Xiong J, Kleindl PA, Hewarathna A, Fisher AC, Joshi SB, Schöneich C, Forrest ML, Middaugh CR, Volkin DB, Deeds EJ

Abstract
There is growing interest in generating physicochemical and biological analytical data sets to compare complex mixture drugs, for example products from different manufacturers. In this work, we compare various crofelemer samples prepared from a single lot by filtration with varying molecular weight cut-offs combined with incubation for different times at different temperatures. The two preceding manuscripts describe experimental data sets generated from analytical characterization of fractionated and degraded crofelemer samples. In this work, we use data mining techniques such as principal component analysis and mutual information scores to help visualize the data and determine discriminatory regions within these large data sets. The mutual information score identifies chemical signatures that differentiate crofelemer samples. These signatures, in many cases, would likely be missed by traditional data analysis tools. We also found that supervised learning classifiers robustly discriminate samples with around 99% classification accuracy, indicating that mathematical models of these physicochemical data sets are capable of identifying even subtle differences in crofelemer samples. Data mining and machine learning techniques can thus identify fingerprint-type attributes of complex mixture drugs that may be used for comparative characterization of products.

PMID: 28743607 [PubMed - as supplied by publisher]

The botanical drug substance crofelemer as a model system for comparative characterization of complex mixture drugs.

Thu, 07/27/2017 - 13:13
Related Articles

The botanical drug substance crofelemer as a model system for comparative characterization of complex mixture drugs.

J Pharm Sci. 2017 Jul 22;:

Authors: Kleindl PA, Xiong J, Hewarathna A, Mozziconacci O, Nariya MK, Fisher AC, Deeds EJ, Joshi SB, Middaugh CR, Schöneich C, Volkin DB, Forrest ML

Abstract
Crofelemer is a botanical polymeric proanthocyanidin that inhibits chloride channel activity and is used clinically for treating HIV-associated secretory diarrhea. Crofelemer lots may exhibit significant physicochemical variation due to the natural source of the raw material. A variety of physical, chemical, and biological assays were utilized to identify potential critical quality attributes (CQAs) of crofelemer, which may be useful in characterizing differently sourced and/or processed drug products. Crofelemer drug substance was extracted from tablets of one commerical drug product lot, fractionated, and subjected to accelerated thermal degradation studies to produce derivative lots with variations in chemical and physical composition potentially representative of manufacturing and raw material variation. Liquid chromatography, UV absorbance spectroscopy, mass spectrometry, and NMR analysis revealed substantial changes in the composition of derivative lots. A chloride channel inhibition cell-based bioassay suggested that substantial changes in crofelemer composition did not necessarily result in major changes to bioactivity. In two companion papers, machine learning and data mining approaches were applied to the analytical and biological data sets presented herein, along with chemical stability data sets derived from forced degradation studies, to develop an integrated mathematical model that can identify CQAs which are most relevent in distinguishing between different populations of crofelemer.

PMID: 28743606 [PubMed - as supplied by publisher]

Modeling complexes of modeled proteins.

Tue, 07/25/2017 - 12:14
Related Articles

Modeling complexes of modeled proteins.

Proteins. 2017 Mar;85(3):470-478

Authors: Anishchenko I, Kundrotas PJ, Vakser IA

Abstract
Structural characterization of proteins is essential for understanding life processes at the molecular level. However, only a fraction of known proteins have experimentally determined structures. This fraction is even smaller for protein-protein complexes. Thus, structural modeling of protein-protein interactions (docking) primarily has to rely on modeled structures of the individual proteins, which typically are less accurate than the experimentally determined ones. Such "double" modeling is the Grand Challenge of structural reconstruction of the interactome. Yet it remains so far largely untested in a systematic way. We present a comprehensive validation of template-based and free docking on a set of 165 complexes, where each protein model has six levels of structural accuracy, from 1 to 6 Å C(α) RMSD. Many template-based docking predictions fall into acceptable quality category, according to the CAPRI criteria, even for highly inaccurate proteins (5-6 Å RMSD), although the number of such models (and, consequently, the docking success rate) drops significantly for models with RMSD > 4 Å. The results show that the existing docking methodologies can be successfully applied to protein models with a broad range of structural accuracy, and the template-based docking is much less sensitive to inaccuracies of protein models than the free docking. Proteins 2017; 85:470-478. © 2016 Wiley Periodicals, Inc.

PMID: 27701777 [PubMed - indexed for MEDLINE]

Structural quality of unrefined models in protein docking.

Tue, 07/25/2017 - 12:14
Related Articles

Structural quality of unrefined models in protein docking.

Proteins. 2017 Jan;85(1):39-45

Authors: Anishchenko I, Kundrotas PJ, Vakser IA

Abstract
Structural characterization of protein-protein interactions is essential for understanding life processes at the molecular level. However, only a fraction of protein interactions have experimentally resolved structures. Thus, reliable computational methods for structural modeling of protein interactions (protein docking) are important for generating such structures and understanding the principles of protein recognition. Template-based docking techniques that utilize structural similarity between target protein-protein interaction and cocrystallized protein-protein complexes (templates) are gaining popularity due to generally higher reliability than that of the template-free docking. However, the template-based approach lacks explicit penalties for intermolecular penetration, as opposed to the typical free docking where such penalty is inherent due to the shape complementarity paradigm. Thus, template-based docking models are commonly assumed to require special treatment to remove large structural penetrations. In this study, we compared clashes in the template-based and free docking of the same proteins, with crystallographically determined and modeled structures. The results show that for the less accurate protein models, free docking produces fewer clashes than the template-based approach. However, contrary to the common expectation, in acceptable and better quality docking models of unbound crystallographically determined proteins, the clashes in the template-based docking are comparable to those in the free docking, due to the overall higher quality of the template-based docking predictions. This suggests that the free docking refinement protocols can in principle be applied to the template-based docking predictions as well. Proteins 2016; 85:39-45. © 2016 Wiley Periodicals, Inc.

PMID: 27756103 [PubMed - indexed for MEDLINE]

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Tue, 07/25/2017 - 12:14
Related Articles

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Proteins. 2016 Sep;84 Suppl 1:323-48

Authors: Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ

Abstract
We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. Proteins 2016; 84(Suppl 1):323-348. © 2016 Wiley Periodicals, Inc.

PMID: 27122118 [PubMed - indexed for MEDLINE]

Using Homology Modeling to Interrogate Binding Affinity in Neutralization of Ricin Toxin by a Family of Single Domain Antibodies.

Wed, 07/19/2017 - 22:04
Related Articles

Using Homology Modeling to Interrogate Binding Affinity in Neutralization of Ricin Toxin by a Family of Single Domain Antibodies.

Proteins. 2017 Jul 18;:

Authors: Bazzoli A, Vance DJ, Rudolph MJ, Rong Y, Angalakurthi SK, Toth RT, Middaugh CR, Volkin DB, Weis DD, Karanicolas J, Mantis NJ

Abstract
In this report we investigated, within a group of closely related single domain camelid antibodies (VH Hs), the relationship between binding affinity and neutralizing activity as it pertains to ricin, a fast-acting toxin and biothreat agent. The V1C7-like VH Hs (V1C7, V2B9, V2E8, and V5C1) are similar in amino acid sequence, but differ in their binding affinities and toxin-neutralizing activities. Using the X-ray crystal structure of V1C7 in complex with ricin's enzymatic subunit (RTA) as a template, Rosetta-based homology modeling coupled with energetic decomposition led us to predict that a single pairwise interaction between Arg29 on V5C1 and Glu67 on RTA was responsible for the difference in ricin toxin binding affinity between V1C7, a weak neutralizer, and V5C1, a moderate neutralizer. This prediction was borne out experimentally: substitution of Arg for Gly at position 29 enhanced V1C7's binding affinity for ricin, whereas the reverse (i.e., Gly for Arg at position 29) diminished V5C1's binding affinity by >10 fold. As expected, the V5C1R29G mutant was largely devoid of toxin-neutralizing activity. However, the toxin-neutralizing activity of the V1C7G29R mutant was not correspondingly improved, indicating that in the V1C7 family binding affinity alone does not account for differences in antibody function. V1C7 and V5C1, as well as their respective point mutants, recognized indistinguishable epitopes on RTA, at least at the level of sensitivity afforded by hydrogen-deuterium mass spectrometry. The results of this study have implications for engineering therapeutic antibodies because they demonstrate that even subtle differences in epitope specificity can account for important differences in antibody function. This article is protected by copyright. All rights reserved.

PMID: 28718923 [PubMed - as supplied by publisher]

Crosstalk and the evolvability of intracellular communication.

Tue, 07/11/2017 - 18:04
Related Articles

Crosstalk and the evolvability of intracellular communication.

Nat Commun. 2017 Jul 10;8:16009

Authors: Rowland MA, Greenbaum JM, Deeds EJ

Abstract
Metazoan signalling networks are complex, with extensive crosstalk between pathways. It is unclear what pressures drove the evolution of this architecture. We explore the hypothesis that crosstalk allows different cell types, each expressing a specific subset of signalling proteins, to activate different outputs when faced with the same inputs, responding differently to the same environment. We find that the pressure to generate diversity leads to the evolution of networks with extensive crosstalk. Using available data, we find that human tissues exhibit higher levels of diversity between cell types than networks with random expression patterns or networks with no crosstalk. We also find that crosstalk and differential expression can influence drug activity: no protein has the same impact on two tissues when inhibited. In addition to providing a possible explanation for the evolution of crosstalk, our work indicates that consideration of cellular context will likely be crucial for targeting signalling networks.

PMID: 28691706 [PubMed - in process]

Chemical stability of the botanical drug substance Crofelemer: a model system for comparative characterization of complex mixture drugs.

Mon, 07/10/2017 - 05:04

Chemical stability of the botanical drug substance Crofelemer: a model system for comparative characterization of complex mixture drugs.

J Pharm Sci. 2017 Jul 05;:

Authors: Hewarathna A, Mozziconacci O, Nariya MK, Kleindl PA, Xiong J, Fisher AC, Joshi SB, Middaugh CR, Forrest ML, Volkin DB, Deeds EJ, Schöneich C

Abstract
As the second of a three part series of articles in this issue concerning the development of a mathematical model for comparative characterization of complex mixture drugs using Crofelemer (CF) as a model compound, this work focuses on the evaluation of the chemical stability profile of CF. CF is a biopolymer containing a mixture of proanthocyanidin oligomers which are primarily composed of gallocatechin with a small contribution from catechin. CF extracted from drug product was subjected to molecular weight-based fractionation and thiolysis. Temperature stress and metal-catalyzed oxidation were selected for accelerated and forced degradation studies. Stressed-CF samples were size fractionated, thiolyzed, and analyzed with a combination of negative-ion electrospray ionization mass spectrometry (ESI-MS) and reversed-phase high pressure liquid chromatography (RP-HPLC) with UV absorption and fluorescence detection. We further analyzed the chemical stability data sets for various CF samples generated from RP-HPLC-UV and ESI-MS using data-mining and machine learning approaches. In particular, calculations based on mutual information of over 800,000 data points in the ESI-MS analytical data set revealed specific CF cleavage and degradation products that were differentially generated under specific storage/degradation conditions, which were not initially identified using traditional analysis of the ESI-MS results.

PMID: 28688843 [PubMed - as supplied by publisher]

The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport.

Sat, 07/01/2017 - 12:17
Related Articles

The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport.

Structure. 2016 Jun 07;24(6):956-64

Authors: McCoy JG, Ren Z, Stanevich V, Lee J, Mitra S, Levin EJ, Poget S, Quick M, Im W, Zhou M

Abstract
The phosphoenolpyruvate:carbohydrate phosphotransferase systems are found in bacteria, where they play central roles in sugar uptake and regulation of cellular uptake processes. Little is known about how the membrane-embedded components (EIICs) selectively mediate the passage of carbohydrates across the membrane. Here we report the functional characterization and 2.55-Å resolution structure of a maltose transporter, bcMalT, belonging to the glucose superfamily of EIIC transporters. bcMalT crystallized in an outward-facing occluded conformation, in contrast to the structure of another glucose superfamily EIIC, bcChbC, which crystallized in an inward-facing occluded conformation. The structures differ in the position of a structurally conserved substrate-binding domain that is suggested to play a central role in sugar transport. In addition, molecular dynamics simulations suggest a potential pathway for substrate entry from the periplasm into the bcMalT substrate-binding site. These results provide a mechanistic framework for understanding substrate recognition and translocation for the glucose superfamily EIIC transporters.

PMID: 27161976 [PubMed - indexed for MEDLINE]

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria.

Tue, 06/27/2017 - 11:07
Related Articles

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria.

Biophys J. 2016 Oct 18;111(8):1750-1760

Authors: Kim S, Patel DS, Park S, Slusky J, Klauda JB, Widmalm G, Im W

Abstract
Lipid A is the lipid anchor of a lipopolysaccharide in the outer leaflet of the outer membrane of Gram-negative bacteria. In general, lipid A consists of two phosphorylated N-acetyl glucosamine and several acyl chains that are directly linked to the two sugars. Depending on the bacterial species and environments, the acyl chain number and length vary, and lipid A can be chemically modified with phosphoethanolamine, aminoarabinose, or glycine residues, which are key to bacterial pathogenesis. In this work, homogeneous lipid bilayers of 21 distinct lipid A types from 12 bacterial species are modeled and simulated to investigate the differences and similarities of their membrane properties. In addition, different neutralizing ion types (Ca(2+), K(+), and Na(+)) are considered to examine the ion's influence on the membrane properties. The trajectory analysis shows that (1) the area per lipid is mostly correlated to the acyl chain number, and the area per lipid increases as a function of the acyl chain number; (2) the hydrophobic thickness is mainly determined by the average acyl chain length with slight dependence on the acyl chain number, and the hydrophobic thickness generally increases with the average acyl chain length; (3) a good correlation is observed among the area per lipid, hydrophobic thickness, and acyl chain order; and (4) although the influence of neutralizing ion types on the area per lipid and hydrophobic thickness is minimal, Ca(2+) stays longer on the membrane surface than K(+) or Na(+), consequently leading to lower lateral diffusion and a higher compressibility modulus, which agrees well with available experiments.

PMID: 27760361 [PubMed - indexed for MEDLINE]

DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites.

Tue, 06/27/2017 - 11:07
Related Articles

DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites.

J Med Chem. 2016 May 12;59(9):4152-70

Authors: Gowthaman R, Miller SA, Rogers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aubé J, Roy A, Karanicolas J

Abstract
Protein-protein interactions represent an exciting and challenging target class for therapeutic intervention using small molecules. Protein interaction sites are often devoid of the deep surface pockets presented by "traditional" drug targets, and crystal structures reveal that inhibitors typically engage these sites using very shallow binding modes. As a consequence, modern virtual screening tools developed to identify inhibitors of traditional drug targets do not perform as well when they are instead deployed at protein interaction sites. To address the need for novel inhibitors of important protein interactions, here we introduce an alternate docking strategy specifically designed for this regime. Our method, termed DARC (Docking Approach using Ray-Casting), matches the topography of a surface pocket "observed" from within the protein to the topography "observed" when viewing a potential ligand from the same vantage point. We applied DARC to carry out a virtual screen against the protein interaction site of human antiapoptotic protein Mcl-1 and found that four of the top-scoring 21 compounds showed clear inhibition in a biochemical assay. The Ki values for these compounds ranged from 1.2 to 21 μM, and each had ligand efficiency comparable to promising small-molecule inhibitors of other protein-protein interactions. These hit compounds do not resemble the natural (protein) binding partner of Mcl-1, nor do they resemble any known inhibitors of Mcl-1. Our results thus demonstrate the utility of DARC for identifying novel inhibitors of protein-protein interactions.

PMID: 26126123 [PubMed - indexed for MEDLINE]

Dynamical predictors of an imminent phenotypic switch in bacteria.

Sat, 06/10/2017 - 14:03
Related Articles

Dynamical predictors of an imminent phenotypic switch in bacteria.

Phys Biol. 2017 Jun 09;:

Authors: Wang H, Ray C

Abstract
Single cells can stochastically switch across thresholds imposed by regulatory networks. Such thresholds can act as a tipping point, drastically changing global phenotypic states. In ecology and economics, imminent transitions across such tipping points can be predicted using dynamical early warning indicators. A typical example is "flickering" of a fast variable, predicting a longer-lasting switch from a low to a high state or vice versa. Considering the different timescales between metabolite and protein fluctuations in bacteria, we hypothesized that metabolic early warning indicators predict imminent transitions across a network threshold caused by enzyme saturation. We used stochastic simulations to determine if flickering predicts phenotypic transitions, accounting for a variety of molecular physiological parameters, including enzyme affinity, burstiness of enzyme gene expression, homeostatic feedback, and rates of metabolic precursor influx. In most cases, we found that metabolic flickering rates are robustly peaked near the enzyme saturation threshold. The degree of fluctuation was amplified by product inhibition of the enzyme. We conclude that sensitivity to flickering in fast variables may be a possible natural or synthetic strategy to prepare physiological states for an imminent transition.

PMID: 28597843 [PubMed - as supplied by publisher]

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface.

Sat, 06/10/2017 - 14:03
Related Articles

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface.

Biophys J. 2016 Jun 21;110(12):2698-709

Authors: Fleming PJ, Patel DS, Wu EL, Qi Y, Yeom MS, Sousa MC, Fleming KG, Im W

Abstract
The outer membrane of Gram-negative bacteria is an asymmetric membrane with lipopolysaccharides on the external leaflet and phospholipids on the periplasmic leaflet. This outer membrane contains mainly β-barrel transmembrane proteins and lipidated periplasmic proteins (lipoproteins). The multisubunit protein β-barrel assembly machine (BAM) catalyzes the insertion and folding of the β-barrel proteins into this membrane. In Escherichia coli, the BAM complex consists of five subunits, a core transmembrane β-barrel with a long periplasmic domain (BamA) and four lipoproteins (BamB/C/D/E). The BamA periplasmic domain is composed of five globular subdomains in tandem called POTRA motifs that are key to BAM complex formation and interaction with the substrate β-barrel proteins. The BAM complex is believed to undergo conformational cycling while facilitating insertion of client proteins into the outer membrane. Reports describing variable conformations and dynamics of the periplasmic POTRA domain have been published. Therefore, elucidation of the conformational dynamics of the POTRA domain in full-length BamA is important to understand the function of this molecular complex. Using molecular dynamics simulations, we present evidence that the conformational flexibility of the POTRA domain is modulated by binding to the periplasmic surface of a native lipid membrane. Furthermore, membrane binding of the POTRA domain is compatible with both BamB and BamD binding, suggesting that conformational selection of different POTRA domain conformations may be involved in the mechanism of BAM-facilitated insertion of outer membrane β-barrel proteins.

PMID: 27332128 [PubMed - indexed for MEDLINE]

Challenges in structural approaches to cell modeling.

Sat, 06/10/2017 - 14:03
Related Articles

Challenges in structural approaches to cell modeling.

J Mol Biol. 2016 Jul 31;428(15):2943-64

Authors: Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA

Abstract
Computational modeling is essential for structural characterization of biomolecular mechanisms across the broad spectrum of scales. Adequate understanding of biomolecular mechanisms inherently involves our ability to model them. Structural modeling of individual biomolecules and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biological networks, imaging data, etc. Structural modeling along with other computational and experimental approaches will provide a fundamental understanding of life at the molecular level and lead to important applications to biology and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual molecules to that of cell biology. Studies in several related areas are covered: biological networks; automated construction of three-dimensional cell models using experimental data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodynamic and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biology, and the prospects of future developments in this emerging field.

PMID: 27255863 [PubMed - indexed for MEDLINE]

Identification of novel small molecule Beclin 1 mimetics activating autophagy.

Thu, 06/08/2017 - 13:03
Related Articles

Identification of novel small molecule Beclin 1 mimetics activating autophagy.

Oncotarget. 2017 May 18;:

Authors: Yu J, Lan L, Lewin SJ, Rogers SA, Roy A, Wu X, Gao P, Karanicolas J, Aubé J, Sun B, Xu L

Abstract
Anti-apoptotic proteins Bcl-2 and Bcl-xL could block autophagy by binding to Beclin 1 protein, an essential inducer of autophagy. Compounds mimicking Beclin 1 might be able to disrupt Bcl-xL/2-Beclin 1 interaction, free out Beclin 1, and thus trigger autophagy. In order to identify small molecule Beclin 1 mimetics, a fluorescence polarization-based high-throughput screening of 50,316 compounds was carried out with a Z' score of 0.82 ± 0.05, and an outcome of 58 hits. After the structure analysis, three acridine analogues were unveiled and confirmed using the fluorescence polarization assay and the surface plasmon resonance assay. Moreover, a set of 17 additional acridine analogues was prepared and tested. Compound 7 showed selectivity for Bcl-xL (KD = 6.5 μM) over Bcl-2 (KD = 160 μM) protein, and potent cytotoxicity (nanomolar scale) in PC-3, PC-3a and DU145 prostate cancer cells. Furthermore, induction of autophagy was also demonstrated in PC-3 and PC-3a cells treated with some acridine compounds by LC3 conversion immunoblotting and LC3 fluorescence microscopy. These Beclin 1 mimetics will be invaluable tools for developing novel autophagy inducers, better understanding the roles of autophagy in cancer, and will contribute to cancer therapy.

PMID: 28591707 [PubMed - as supplied by publisher]


One of 34 U.S. public institutions in the prestigious Association of American Universities
44 nationally ranked graduate programs.
—U.S. News & World Report
Top 50 nationwide for size of library collection.
—ALA
23rd nationwide for service to veterans —"Best for Vets," Military Times
KU Today