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Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

Charuvaka Muvva, Natarajan Arul Murugan, Venkatesan Subramanian
2021 International Journal of Molecular Sciences  
The study also included a poly-alanine sequence as a reference system.  ...  For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures.  ...  However, in the case of parallel and anti-parallel dimeric structures, the β-sheet structure is found to be more stable due to the possibility to make many intermolecular hydrogen bonds.  ... 
doi:10.3390/ijms22063244 pmid:33806726 fatcat:ezoqb5spobgj7kxfkugt6ezyoi

Application of the PM6 method to modeling proteins

James J. P. Stewart
2008 Journal of Molecular Modeling  
The applicability of the newly developed PM6 method for modeling proteins is investigated.  ...  In order to allow the geometries of such large systems to be optimized rapidly, three modifications were made to the conventional semiempirical procedure: the matrix algebra method for solving the self-consistent  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided  ... 
doi:10.1007/s00894-008-0420-y pmid:19066990 fatcat:rht3wsnbdze47hc6edynepy35a

Computer design of idealized β‐motifs

Andrzej Kolinski, Wojciech Galazka, Jeffrey Skolnick
1995 Journal of Chemical Physics  
A lattice model of protein conformation and dynamics is used to explore the requirements for the de novo folding from an arbitrary random coil state of idealized models of four and six-member ␤-barrels  ...  A number of possible conjectures for the factors giving rise to the structural uniqueness of globular proteins are examined.  ...  In particular, by including the positions of the amide hydrogens and carbonyl oxygens in the calculation of the hydrogen bond energy, the registration of both parallel and antiparallel ␤-sheets is substantially  ... 
doi:10.1063/1.469930 fatcat:vweiwzuxyffsxehtjy7sc7tety

A computational study of the self-assembly of the RFFFR peptide

Morten Slyngborg, Peter Fojan
2015 Physical Chemistry, Chemical Physics - PCCP  
A multi-level computational investigation of the self-assembly of the peptide, RFFFR, into nano-fibers.  ...  studies indicate that nanostructures self-assembled from the FF or FFF peptide consist of a high degree beta-sheet. 8, 12 Presumably this deviation is due to the limited simulation time and number of  ...  Our findings conform with the majority of experimental and computational studies indicating that the T-shaped mode is more stable than the PD mode in proteins. 68 However, we also observe a more complex  ... 
doi:10.1039/c5cp01324k pmid:26499975 fatcat:3jkhbypj65hkzeu5zlwys2uif4

Self-consistently optimized statistical mechanical energy functions for sequence structure alignment

K. K. Koretke, Z. Luthey-Schulten, P. G. Wolynes
2008 Protein Science  
The lowest energy alignment generated with the energy function for sequences containing prosite signatures but unknown structures is a structure containing the same prosite signature, providing a check  ...  or similarity as scoring parameters.  ...  Acknowledgments We thank Professor Harry Gray and Ben Ramirez for inspirational discussions and input on the experimental chemical constraints for copper A domain of cytochrome c oxidase.  ... 
doi:10.1002/pro.5560050607 pmid:8762136 pmcid:PMC2143433 fatcat:6qe34jbymjhr5ogqgwi442cpbq

DichroCalc--circular and linear dichroism online

B. M. Bulheller, J. D. Hirst
2009 Bioinformatics  
A note on versions: The version presented here may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher's version.  ...  Preface Linear dichroism (LD) provides information on the orientation of molecules but is more challenging to analyze than CD.  ...  In β-sheets the π → π * transition is polarized parallel to the long axis of a single strand (perpendicular to the sheet), due to the lack of the parallel component at ∼210 nm. 51 In actuality, about  ... 
doi:10.1093/bioinformatics/btp016 pmid:19129206 fatcat:6ijxxpdt7jf7ncd4vwiwhpxriy

The Use of Circular Dichroism in the Investigation of Protein Structure and Function

Sharon Kelly, Nicholas Price
2000 Current protein and peptide science  
It is therefore evident that CD is a versatile technique in structural biology, with an increasingly wide range of applications.  ...  In the far UV region (240-180 nm), which corresponds to peptide bond absorption, the CD spectrum can be analysed to give the content of regular secondary structural features such as α-helix and β-sheet  ...  Andy Freer, Steve Prince and Jeremy Beauchamp for help in obtaining a copy of the structure of the LH2 complex.  ... 
doi:10.2174/1389203003381315 pmid:12369905 fatcat:mdpe5scixzcmnhrxbep5ek5i2u

Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules

Marco Marazzi, Hugo Gattuso, Antonio Monari, Xavier Assfeld
2018 Frontiers in Chemistry  
with external dyes-often drugs or pollutants-that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages.  ...  The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature  ...  ACKNOWLEDGMENTS The authors would like to gratefully thank the Phi-Science student association for providing an adequate working space to the authors while they wrote this manuscript.  ... 
doi:10.3389/fchem.2018.00086 pmid:29666792 pmcid:PMC5891624 fatcat:lzi63rofyzh3vde5hvvevipuby

Conformation of Polypeptides and Proteins [chapter]

G.N. Ramachandran, V. Sasisekharan
1968 Advances in Protein Chemistry  
As the mole fraction of V is increased, the helicity decreased.  ...  Here again ORD studies indicated that all polymers studied adopt a certain amount of helical conformation in solution. Infrared spectra of films indicated the same results.  ...  Pair of Polypeptide Chains in the Parallel and Antiparallel Pleated Sheet Arrangements Parallel pleated sheet (h = 6.50 d) Antiparallel pleapd sheet (h = 7.00 A) Energy (kcal/mole/residue) Energy  ... 
doi:10.1016/s0065-3233(08)60402-7 fatcat:w4r7i4o4pvfsdexpolak3uoqhm

MAGNETOHYDRODYNAMIC WAVES AND CORONAL HEATING: UNIFYING EMPIRICAL AND MHD TURBULENCE MODELS

Igor V. Sokolov, Bart van der Holst, Rona Oran, Cooper Downs, Ilia I. Roussev, Meng Jin, Ward B. Manchester, Rebekah M. Evans, Tamas I. Gombosi
2013 Astrophysical Journal  
We present a new global model of the solar corona, including the low corona, the transition region and the top of chromosphere.  ...  The distinctive feature of the new model is incorporating the MHD Alfven wave turbulence.  ...  R.M.E. is supported through an appointment to the NASA Postdoctoral Program at GSFC, administered by Oak Ridge Associated Universities through a contract with NASA.  ... 
doi:10.1088/0004-637x/764/1/23 fatcat:j5s3pzexn5bztmzmhi5nvvqkp4

De novo and inverse folding predictions of protein structure and dynamics

Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick
1993 Journal of Computer-Aided Molecular Design  
Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered [3-barrel proteins, it is shown that idealized fingerprints constructed from simple  ...  The first is a one-body, amino-acid-specific potential of mean force which depends on the distance of the center of the side A B J Fig. 12.  ...  The first one is an ideal fragment of the contact pattern for two parallel a-helices. The second one is for two antiparallel, and the third one for two p-strands.  ... 
doi:10.1007/bf02337559 pmid:8229093 fatcat:eo5brg46ljfo7p54zvbsb32kv4

Mechanical Processes in Biochemistry

Carlos Bustamante, Yann R. Chemla, Nancy R. Forde, David Izhaky
2004 Annual Review of Biochemistry  
ϫ 10 Ϫ5 or 1.9 ϫ 10 Ϫ6 Parallel ␤-sheet shear (23, 46) 10 FNIII domain from fibronectin - 74 Ϯ 20 0.38 2.0 ϫ 10 Ϫ2 Antiparallel ␤-sheet shear (14, 35) C2A domain -  ...  (100) studied strain in the carbonyl bond of the substrate of beta-lactamase.  ... 
doi:10.1146/annurev.biochem.72.121801.161542 pmid:15189157 fatcat:gv53zzs3cjga5draoghxeeggmu

Abstracts of the 29th Annual Symposium of The Protein Society

2015 Protein Science  
Several studies have described production of QDs from biological systems, but without control over particle size or composition.  ...  Nuclear magnetic resonance (NMR) is a powerful biophysical method for studying protein-ligand interactions in solution and elucidating the mechanism of action of potential inhibitors.  ...  Kyungpook National University Scolopendin 2, AGLQFPVGRIGRLLRK, is a 16-mer peptide derived from the centipede Scolopendra subspinipes mutilans.  ... 
doi:10.1002/pro.2823 pmid:26452528 pmcid:PMC4632850 fatcat:ejmksoqj3zbsrkabl4jyp7emgi

Extended MHD modeling of the steady solar corona and the solar wind

Tamas I. Gombosi, Bart van der Holst, Ward B. Manchester, Igor V. Sokolov
2018 Living Reviews in Solar Physics  
The history and present state of large-scale magnetohydrodynamic modeling of the solar corona and the solar wind with steady or quasi-steady coronal physics is reviewed.  ...  This historical perspective is also applied to the present suite of global corona and solar wind models.  ...  As seen in Fig. 22, for regions of low plasma beta, such as coronal holes, most energy goes to perpendicular proton heating, while in high beta regions, such as the current sheet, parallel heating dominates  ... 
doi:10.1007/s41116-018-0014-4 pmid:30872981 pmcid:PMC6390891 fatcat:kfecykjbjfg4vo5mvcv5uiste4

Thirty-Fourth Annual Meeting February 18–22, 1990 Baltimore Convention Center Baltimore, Maryland

1990 Biophysical Journal  
The phosphopeptide is sensitive to ADP but not to K , and is more stable (to.5=8 min; OC; pH 7) than the native EP.  ...  The beta subunit is not differentially labelled by PLP in presence or absence of ATP.  ...  We have extended these studies to determine whether a tyrosinate is formed in the light-adapted protein (bR5s68) or the M photointermediates.  ... 
doi:10.1016/s0006-3495(90)82549-2 fatcat:izo6b6i77fhovhtartgh4c2bra
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