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The Mechanism for Acetylcholine Receptor Inhibition by α-Neurotoxins and Species-Specific Resistance to α-Bungarotoxin Revealed by NMR

Abraham O. Samson, Tali Scherf, Miriam Eisenstein, Jordan H. Chill, Jacob Anglister
2002 Neuron  
according to alignment with ␣1) binds ␣-BTX spectroscopy.  ...  Snake venom ␣-neurotoxins and other 'threefinger' proteins. Eur. J. Biochem. 264, 281-286.  ...  Torsion-angle constraints included 77 quence identity with ␣7. Superposition of the toxin φ-angles and 41 1 -angles.  ... 
doi:10.1016/s0896-6273(02)00773-0 pmid:12160749 fatcat:uvwi5nv67jabhggcntddnpljya

Multiple structure alignment with msTALI

Paul Shealy, Homayoun Valafar
2012 BMC Bioinformatics  
Our algorithm uses several informative features to guide its alignments: torsion angles, backbone C α atom positions, secondary structure, residue type, surface accessibility, and properties of nearby  ...  A method that is capable of solving a variety of problems using structure comparison is still absent. Here we introduce a program msTALI for aligning multiple protein structures.  ...  Other researchers have used backbone φ and ψ torsion angles [19] , while TALI [20] incorporates torsion angles and sequence information and Lesk [21] uses torsion angles and a reduced residue representation  ... 
doi:10.1186/1471-2105-13-105 pmid:22607234 pmcid:PMC3473313 fatcat:w5g57grjkjeupdpyxacv3kegyi

Validity of Protein Structure Alignment Method Based on Backbone Torsion Angles

Sunghoon Jung, Se- Eun Bae
2011 Journal of Proteomics & Bioinformatics  
Gapless global alignment between protein structures was conducted to validate the effectiveness of performing structural alignment with strings of backbone torsion angles.  ...  However, performance of the backbone dihedral angle alignment was not supported with sufficiently large test sets to be quantified; i.e. only 2 pairs or 4 pairs of proteins were analyzed.  ...  Thus, we used functional classification of proteins as our classification reference, focusing more on the practical utility of the backbone torsion angle based structure alignment algorithm to correctly  ... 
doi:10.4172/jpb.1000192 fatcat:m26fxnxdjnflbpkc5yaz5oxmwu

Aligning Multiple Protein Structures using Biochemical and Biophysical Properties [article]

Paul Shealy, Homayoun Valafar
2019 arXiv   pre-print
We have developed an algorithm (msTALI) for aligning multiple protein structures using biochemical and biophysical properties, including torsion angles, secondary structure, hydrophobicity, and surface  ...  Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in  ...  and extends previous work on pairwise structure alignment using torsion angles [11] .  ... 
arXiv:1911.02406v1 fatcat:fhovzqm7tvhrbna6qldgjhirta

Mimicking the Structure of the V3 Epitope Bound to HIV-1 Neutralizing Antibodies†

Amit Mor, Eugenia Segal, Brenda Mester, Boris Arshava, Osnat Rosen, Fa-Xiang Ding, Joseph Russo, Amnon Dafni, Fabian Schvartzman, Tali Scherf, Fred Naider, Jacob Anglister
2009 Biochemistry  
The V3 sequence determines whether the virus will manifest R5 or ×4 phenotypes and use the CCR5 or C×CR4 chemokine co-receptor, respectively.  ...  Incorporation of a second disulfide bond results in significant overall rigidity and in one case, a structure close to that of V3 MN peptide bound to 447-52D Fab was assumed and in another case a structure  ...  Bond length (Å) 0.0008±0.0001 Bond angles (º) 0.323±0.003 Improper angles 0.089±0.005 Distance constraint violoation * Number > 0.1Å 5+1 Maximum (Å) 0.22+0.03 Torsion angle violation  ... 
doi:10.1021/bi802308n pmid:19281264 pmcid:PMC2756766 fatcat:fuwva5pq7zh7zdlrqfpkmyjj4q

Alternative Conformations of HIV-1 V3 Loops Mimic β Hairpins in Chemokines, Suggesting a Mechanism for Coreceptor Selectivity

Michal Sharon, Naama Kessler, Rina Levy, Susan Zolla-Pazner, Matthias Görlach, Jacob Anglister
2003 Structure  
This study was supported by the Minwere used for epitope mapping.  ...  Tali Scherf for help in the NMR experiments, labeled with 15 N or with 13 C and 15 N in complex with unlabeled 447 and Dr. Mirek Gorny for the immunological characterization of 447-Fv.  ...  as recogno NOE violations larger than 0.5 Å and no torsion angle nized by the Fv fragment of the HIV-1-neutralizing huviolations exceeding 5Њ is shown in Figure 2A .  ... 
doi:10.1016/s0969-2126(03)00011-x pmid:12575942 fatcat:45euhk6tqvggxovepzph2pvxge

Structural basis for cooperative interactions of substituted 2-aminopyrimidines with the acetylcholine binding protein

K. Kaczanowska, M. Harel, Z. Radi, J.-P. Changeux, M. G. Finn, P. Taylor
2014 Proceedings of the National Academy of Sciences of the United States of America  
S2B ) rather than the dihedral angles for torsional movement (twist) (SI Appendix, Fig. S2C ).  ...  Structure alignment (UCSF Chimera) of Ls-AChBP with GLIC X-ray crystal structures superimposed terminal residue 205 of Ls-AChBP complex with residue 194 of GLIC, which is located in the protein vestibule  ...  Dihedral angles (α , Fig.  ... 
doi:10.1073/pnas.1410992111 pmid:25006260 pmcid:PMC4115551 fatcat:7mhdpffcjjgqxg6nhebc5hoawu

A Predicted Binding Site for Cholesterol on the GABAA Receptor

Jérôme Hénin, Reza Salari, Sruthi Murlidaran, Grace Brannigan
2014 Biophysical Journal  
Using our models, we investigate cholesterol binding to intersubunit cavities of the GABA A R transmembrane domain.  ...  Current data on structurally related modulators suggest that cholesterol binds to subunit interfaces between transmembrane domains of the GABA A R.  ...  Antoine Taly for many fruitful discussions. We also acknowledge use of computational resources from the National Science Foundation  ... 
doi:10.1016/j.bpj.2014.03.024 pmid:24806926 pmcid:PMC4017285 fatcat:bp2wk6e4vnfr5h53kadfotio7i

Thirtieth Annual Meeting 9–13 February 1986 Brooks Hall/Convention Center, San Francisco, California

1986 Biophysical Journal  
A commercially-available microcomputer-based spreadsheet program is used to ease the interpretation of analytical ultracentrifuge data in three ways: protein amino acid composition is used to calculate  ...  The primary structure of the 30,000-d pore-forming protein of the mitochondrial outer membrane (called VDAC or porin) has recently been derived from the cDNA sequence of yeast (Mihara and Sato 1985 EMBO  ...  The negative CD bands maxi-mizeatQ=300 and 850, coincidental with angles found most often in globular protein structures.  ... 
doi:10.1016/s0006-3495(86)83679-7 fatcat:pkqszgqkg5gk7abm7n7zvahrla

Forty-First Annual Meeting March 2-6, 1997 Ernest N. Morial Convention Center New Orleans, Louisiana. Tuesday Symposia and Posters, Part IV

1997 Biophysical Journal  
MYfOSIN The bisindolymaleimide, Ro 31-8220, is thought to be a specific inhibitor of protein kinase C (PKC).  ...  We suggest that phosphorylation of MLC2o can affect the structure of extended, 6S myosin. Medical School Worcester, MA 01655.0127.  ...  This background was riddled with the second structure, fractures containing aligned micelies.  ... 
doi:10.1016/s0006-3495(97)78739-3 fatcat:5r4yzizegffk7mdykunie2vf3u

Structural and functional characterization of surface proteins from pathogenic bacteria

Maria Antonietta Gentile
Another system for the secondary structure prediction is TALOS+ (Torsion Angle Likelihood Obtained from Shift and sequence similarity) which allowed to predict phi and psi backbone torsion angles using  ...  In this algorithm, the molecular dynamics simulation uses torsion angles as degree of freedom, while bond lengths, angles, and backbone peptide plane angles are fixed.  ... 
doi:10.6092/unina/fedoa/8799 fatcat:65uwkyqarzf23kge52e7esrf4q


Valentina Gargiulo
Based on of the chemical structure backbone, there are four classes of GAGs: Hyaluronan (HA), Heparin (HP)/Heparan sulfate (HS), Chondroitin (CS)/Dermatan sulfate (DS) and Keratan sulfate (KS).  ...  Despite their simple backbone sequence, glycosaminoglycans are complex molecules characterized by a heterogeneous structure, for this reason the investigation on them is really challenging and it is performed  ...  The connections (1→2), (1→3), and (1→4) can be fully described by the two torsion angles Φ and Ψ, whereas the connection (1→6) needs a third torsion angle ω.  ... 
doi:10.6092/unina/fedoa/4191 fatcat:wyyoerourzawzd5hqf7mhrdnse

Kimdaejung Convention Center

2019 2019 IEEE 13th International Conference on Nano/Molecular Medicine & Engineering (NANOMED)  
Further, we discuss the structure of silk and its remarkable properties. Improving antibacterial properties using laser/plasma strategies and growing graphene oxide coatings will be discussed.  ...  Liposomes are clinically used as drug carriers for cancer therapy, however, unwanted leakage of the encapsulated anti-cancer drug and poor tumor-targeting efficiency of liposomes may generate toxic side  ...  The bioactive glass was synthesized using sol-gel method. Pluronic F-127 was used as ink carrier for fabricating the scaffolds.  ... 
doi:10.1109/nanomed49242.2019.9130603 fatcat:wlmmq4uwyjablibepjnazw4fp4

The Second National Festival & International Congress on Stem Cell & Regenerative Medicine - 13-15 July, 2017

2017 Iranian Journal of Biotechnology  
/de torsion mice.  ...  Structures of the obtained scaffolds were characterized by FTIR (Figure 1b) . The characteristic peaks of PCL and PLA are similar due to the polyester backbone.  ...  The advantage of incorporating various CNWs is to have tunable mechanical properties and biodegradability due to variety in their structure.  ... 
doi:10.15171/ijb.2017.s1-334 fatcat:hvotzduiebcg7ppx4q656vljxq

Structural and dynamical properties of central nervous system proteins with pharmaceutical and biotechnological potential

Francesca Stanzione
In this framework, the main scopes of the present PhD project have been the analysis of structural/dynamic determinants of the function of neuroprotective proteins (neurotrophins) and the study of structural  ...  Neurotrophins (NTs) are homodimeric proteins that play a key role in the differentiation, survival and maintenance of nerve cells.  ...  The intra-molecular potential energy is typically represented by harmonic oscillators for bond stretching and angle bending, a Fourier series for each torsional angle, and Coulomb and Lennard-Jones (LJ  ... 
doi:10.6092/unina/fedoa/8027 fatcat:t5b33n77unazzlz5f545kqnbma
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