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In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b [article]

Shahram Mesdaghi, David L Murphy, Filomeno Sánchez Rodríguez, J. Javier Burgos-Mármol, Daniel J Rigden
2020 bioRxiv   pre-print
Here we use evolutionary covariance-derived information not only to construct and validate ab initio models but also to make domain boundary predictions and infer local structural features.  ...  Ab initio modelling of Tmem41b reinforces these structural predictions. Local structural features predicted to be present in Tmem41b are also present in Cl-/H+ antiporters.  ...  Until the structure of poorly characterised protein families such as Pfam family PF09335 can be elucidated experimentally, ab initio protein modelling can be used to predict a fold allowing for structure-based  ... 
doi:10.1101/2020.06.27.174763 fatcat:p23ewv75tveolafphgyfbnbaom

Single-spanning transmembrane domains in cell growth and cell-cell interactions

Pierre Hubert, Paul Sawma, Jean-Pierre Duneau, Jonathan Khao, Jélerôme Hénin, Dominique Bagnard, James Sturgis
2010 Cell Adhesion & Migration  
as transmembrane or peripheral, the membrane-spanning domains being structured as beta-sheets in bacteria and mitochondria or in majority as alpha helices.  ...  The importance of membrane proteins cannot be underestimated as they account for 25-30% of all proteins (ORFs) identified in sequenced genomes in eukaryotes and prokaryotes. 1,2 They can be classified  ...  In conclusion, biases in structural databases toward polytopic membrane proteins and difficulties of interpretation of evolutionary data for bitopic proteins limits the usefulness of ab initio approaches  ... 
doi:10.4161/cam.4.2.12430 pmid:20543559 pmcid:PMC2900628 fatcat:nlrykq3zb5gzveeflw4srrwnji

Ab initio Designed Antimicrobial Peptides Against Gram-Negative Bacteria

Shravani S. Bobde, Fahad M. Alsaab, Guangshuan Wang, Monique L. Van Hoek
2021 Frontiers in Microbiology  
We designed eight novel AMPs, termed PHNX peptides, using ab initio computational design (database filtering technology combined with the novel positional analysis on APD3 dataset of AMPs with activity  ...  Laboratory-based experimental results were compared to computationally predicted activities for each of the peptides to ascertain the accuracy of the computational tools used.  ...  neural network (ANN) and discriminate analysis (DA)] were used to assess PHNX AMPs predicted antimicrobial activity.  ... 
doi:10.3389/fmicb.2021.715246 pmid:34867843 pmcid:PMC8636942 fatcat:egbamwppmbcvrer24kgde4bw5y

Functional pangenome analysis provides insights into the origin, function and pathways to therapy of SARS-CoV-2 coronavirus [article]

Intikhab Alam, Allan K Kamau, Maxat Kulmanov, Stefan T Arold, Arnab T Pain, Takashi Gojobori, Carlos M. Duarte
2020 biorxiv/medrxiv   pre-print
We then annotate the functions, which are confirmed by structural analysis, and predict the potential location within the host cells of these proteins.  ...  detection of COVID-2019 be developed based on the SARS-CoV-2 E protein and that treatment using mutated SARS-Cov-2 lacking the E protein be explored as a promising candidate for a vaccine.  ...  We used all genes from Betacoronavirus dataset in order to explore Gene Ontology predictions through our in-house DeepGOPlus 18 tool that combines deep convolutional neural network (CNN) model with sequence  ... 
doi:10.1101/2020.02.17.952895 fatcat:osx7eje7qbhnhp3kjupjdzr2m4

Dynamics-based Alignment: A Novel Tool For Comparing Large-scale Movements In Proteins With Same Or Different Fold

Andrea Zen, Vincenzo Carnevale, Arthur M. Lesk, Cristian Micheletti
2009 Biophysical Journal  
It has been noted that in mammals and higher organisms, the BAR domain with an N-terminal amphipathic helix and BAR domain (N-BAR) can drive the membrane curvature both in vivo and in vitro.  ...  Their interactions with the WD domain were studied and optimized using Deep View program and the Swiss-Model server.  ...  In addition, we predict a target-specific weighting factor optimal for a target sequence by an artificial neural network from features of the target sequence.  ... 
doi:10.1016/j.bpj.2008.12.3444 fatcat:ac6vqyebtrgptnxqxvbhsfg6me

Homology Modeling and Molecular Dynamics Simulation Studies of the human resistin protein

Chilamakuri C. Sekhar Reddy, Ramanathan Sowdhamini, Bernard Offmann
2009 Biophysical Journal  
It has been noted that in mammals and higher organisms, the BAR domain with an N-terminal amphipathic helix and BAR domain (N-BAR) can drive the membrane curvature both in vivo and in vitro.  ...  Their interactions with the WD domain were studied and optimized using Deep View program and the Swiss-Model server.  ...  In addition, we predict a target-specific weighting factor optimal for a target sequence by an artificial neural network from features of the target sequence.  ... 
doi:10.1016/j.bpj.2008.12.3446 fatcat:4kz25ntwevbsbgwguwotrcztj4

Knowledge based structure prediction of the light-harvesting complex II of rhodospirillum molischianum [chapter]

Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Juergen Koepke, Hartmut Michel
1995 Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding  
We illustrate in this article how one proceeds to predict the structure of integral membrane proteins using a combined approach in which molecular dynamics simulations and energy minimization are performed  ...  We focus here on the prediction of the structure of the light-harvesting complex II (LH-II) of Rhodospirillum molischianum, an integral membrane protein of 16 polypeptides aggregating and binding to 24  ...  method (SOPM) for protein secondary structure prediction [GD94] . b: Neural network based informational approach for protein secondary structure prediction [HK91] .  ... 
doi:10.1090/dimacs/023/07 dblp:conf/dimacs/HuXHSKM95 fatcat:7qxqflozxrdtbggotapiv3jfny

Prediction of the Structure of an Integral Membrane Protein: The Light-Harvesting Complex II of Rhodospirillum molischianum [chapter]

Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Juergen Koepke, Hartmut Michel
1996 Biological Membranes  
We illustrate in this chapter how one proceeds to predict the structure of integral membrane proteins when a highly homologous structure is unknown.  ...  We focus here on the prediction of the structure of the light-harvesting complex II (LH-II) of Rhodospirillum molischianum, an integral membrane protein of 16 polypeptides aggregating and binding to 24  ...  If successful, this work will be the first using an ab initio predicted structure as a probe structure in the framework of molecular replacement to solve the phase problem in X-ray crystallography structure  ... 
doi:10.1007/978-1-4684-8580-6_15 fatcat:ab53uen4urf23dj3fpx33ae3oq

Functional Pangenome Analysis Shows Key Features of E Protein Are Preserved in SARS and SARS-CoV-2

Intikhab Alam, Allan A. Kamau, Maxat Kulmanov, Łukasz Jaremko, Stefan T. Arold, Arnab Pain, Takashi Gojobori, Carlos M. Duarte
2020 Frontiers in Cellular and Infection Microbiology  
The S proteins from SARS and SARS-CoV-2 are similar, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-specific neutralizing antibodies to inhibit SARS-CoV-2.  ...  Here we used comparative pangenomic analysis of all sequenced reference Betacoronaviruses, complemented with functional and structural analyses.  ...  (ab initio structure predictions) (Xu and Zhang, 2012) .  ... 
doi:10.3389/fcimb.2020.00405 pmid:32850499 pmcid:PMC7396417 fatcat:seowgiqpxnfkzfia6szqmnewte

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

Adrian L Sanborn, Benjamin T Yeh, Jordan T Feigerle, Cynthia V Hao, Raphael J L Townshend, Erez Lieberman-Aiden, Ron O Dror, Roger D Kornberg
2021 eLife  
Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes.  ...  ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints.  ...  Clearly, full sequence 172 information beyond aa composition is needed to predict activation. 173 We therefore trained a deep convolutional neural network (CNN) to predict activation 174 based on protein  ... 
doi:10.7554/elife.68068 pmid:33904398 pmcid:PMC8137143 fatcat:ojj7mlzf55hy3l2akds3p74i6i

第57回年会予稿集

2019 Seibutsu Butsuri  
Using these data, we have developed methods for prediction of protein contacts and protein-ligand interactions based on deep neural networks.  ...  In this study, we designed amphipathic α-helix peptides based on two different helix packing motif: GxxxG and GxxxxxxG.  ...  First, we synthesized HaloTag fluorescence ligand conjugated with several glycans, and introduced to membrane proteins.  ... 
doi:10.2142/biophys.59.s1 fatcat:rsudhlmaanetrhmdxjgsiyorme

Strategies in Translating the Therapeutic Potentials of Host Defense Peptides

Darren Shu Jeng Ting, Roger W. Beuerman, Harminder S. Dua, Rajamani Lakshminarayanan, Imran Mohammed
2020 Frontiers in Immunology  
However, the mission of translating novel HDP-derived molecules from bench to bedside has yet to be fully accomplished, primarily attributed to their intricate structure-activity relationship, toxicity  ...  substitution with natural and/or unnatural amino acids, hybridization, L-to-D heterochiral isomerization, C- and N-terminal modification, cyclization, incorporation with nanoparticles, and "smart design" using  ...  networks, and improvement in AI algorithms using machine learning and deep learning (177) (178) (179) (180) .  ... 
doi:10.3389/fimmu.2020.00983 pmid:32528474 pmcid:PMC7256188 fatcat:r6iqtrt2uvdj7o2fjaqrm356pi

Thirty-eighth Annual Meeting March 6-10, 1994 New Orleans Convention Center New Orleans, Louisiana. Monday Symposia and Posters, Part IV

1994 Biophysical Journal  
Recent data on protein synthetic patterns showed elevated levels of "heat shock" proteins in samples exposed to either EM fields or elevated temperature.  ...  Experiments have used dipteran salivary gland cells, yeast and human HL-60 cells.  ...  M-Pos209 PREDICTION OF TRANSMEMBRANE DOMAINS OF PROTEINS WITH NEURAL NETWORKS.  ... 
doi:10.1016/s0006-3495(94)80815-x fatcat:5qyysizpgfhophydgtu4nofoyq

Thirty-third Annual Meeting February 12 - 16, 1989 Albert B. Sabin Convention Center Cincinnati, Ohio

1989 Biophysical Journal  
ILAs have the predicted structure and dimensions and form in large numbers only in systems with the predicted range of interfacial curvature [2,3].  ...  isotropic structure.  ...  neural network in addition to its use in a variety of other parallel computational schemes.  ... 
doi:10.1016/s0006-3495(89)82827-9 fatcat:qfdufjf4uvdkbkucpiwdv6xs3m

Plant Antimicrobial Peptides as Potential Tool for Topic Treatment of Hidradenitis Suppurativa

Carlos André dos Santos-Silva, Paola Maura Tricarico, Lívia Maria Batista Vilela, Ricardo Salas Roldan-Filho, Vinícius Costa Amador, Adamo Pio d'Adamo, Mireli de Santana Rêgo, Ana Maria Benko-Iseppon, Sergio Crovella
2021 Frontiers in Microbiology  
HS is characterized by suppurative skin lesions in diverse body areas, including deep-seated painful nodules, abscesses, draining sinus, and bridged scars, among others, with typical topography.  ...  For this purpose, different classes of drugs, including anti-inflammatory molecules, antibiotics and biological drugs are being used.  ...  -Methods based on computational prediction: Known peptides available in databases can be used as models to predict AMP activity with the aid of predictive algorithms (as neural networks, genetic algorithms  ... 
doi:10.3389/fmicb.2021.795217 pmid:34966375 pmcid:PMC8710806 fatcat:6aka7s3elngqzk7ukxs2ppiswy
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