scholarly journals Finding low-energy conformations of lattice protein models by quantum annealing

2012 ◽  
Vol 2 (1) ◽  
Author(s):  
Alejandro Perdomo-Ortiz ◽  
Neil Dickson ◽  
Marshall Drew-Brook ◽  
Geordie Rose ◽  
Alán Aspuru-Guzik
Keyword(s):  
Low Energy ◽  
Quantum Annealing ◽  
Protein Models ◽  
Lattice Protein Models ◽  
Low Energy Conformations

STUDIES OF FINDING LOW ENERGY CONFIGURATIONS IN OFF-LATTICE PROTEIN MODELS

2006 ◽  
Vol 05 (03) ◽  
pp. 587-594 ◽  
Author(s):  
JINGFA LIU ◽  
WENQI HUANG
Keyword(s):  
Lower Energy ◽  
Gradient Descent ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Ground States ◽  
Low Energy ◽  
Protein Models ◽  
Energy Configurations ◽  
Energy Landscape Paving ◽  
Lattice Protein Models

We studied two three-dimensional off-lattice protein models with two species of monomers, hydrophobic and hydrophilic. Low energy configurations in both models were optimized using the energy landscape paving (ELP) method and subsequent gradient descent. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. For all sequences with lengths 13 ≤ n ≤ 55, the algorithm finds states with lower energy than previously proposed putative ground states.

scholarly journals THE STRUCTURE OF THE FREE ENERGY SURFACE OF COARSE-GRAINED OFF-LATTICE PROTEIN MODELS

2007 ◽  
Vol 18 (01) ◽  
pp. 99-106 ◽  
Author(s):  
ETHEM AKTÜRK ◽  
HANDAN ARKIN ◽  
TARIK ÇELİK
Keyword(s):  
Energy Surface ◽  
Energy Landscape ◽  
Low Energy ◽  
Coarse Grained ◽  
Free Energy Surface ◽  
Protein Model ◽  
Energy Part ◽  
Folding Pathways ◽  
Protein Models ◽  
Lattice Protein Models

We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method samples the whole rugged energy landscape, in particular the low-energy part, and enables one to better understand the critical behaviors and visualize the folding pathways of the considered protein model.

Spatial Structure of the Acth-(6-9)-PGP Molecule

2021 ◽  
Vol 43 (5) ◽  
pp. 500-500
Author(s):  
Namiq Akhmedov Namiq Akhmedov ◽  
Leyla Agayeva Leyla Agayeva ◽  
Gulnara Akverdieva Gulnara Akverdieva ◽  
Rena Abbasli and Larisa Ismailova Rena Abbasli and Larisa Ismailova
Keyword(s):  
Amino Acid ◽  
Spatial Structure ◽  
Main Chain ◽  
Low Energy ◽  
Dihedral Angles ◽  
Amino Acid Residues ◽  
Analysis Method ◽  
Theoretical Conformational Analysis ◽  
Energy Of Hydrogen Bonds ◽  
Low Energy Conformations

The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

scholarly journals Enzyme-hydrolyzed Fruit of Jurinea mollis: A Rich Source of (-)-(8R,8′R)-Arctigenin

2016 ◽  
Vol 11 (10) ◽  
pp. 1934578X1601101 ◽  
Author(s):  
Rita Könye ◽  
Ágnes Evelin Ress ◽  
Anna Sólyomváry ◽  
Gergő Tóth ◽  
András Darcsi ◽  
...  
Keyword(s):  
Low Energy ◽  
Plant Tissues ◽  
Selective Isolation ◽  
Isolation Method ◽  
Specific Accumulation ◽  
Fruit Wall ◽  
Lignan Glycoside ◽  
Nmr Methods ◽  
First Time ◽  
Low Energy Conformations

In Jurinea mollis fruit, the dibenzylbutyrolactone-type lignan glycoside arctiin and its aglycone arctigenin were determined for the first time using a combination of optimized enzymatic treatment and complementary spectrometric (HPLC-MS, GC-MS) and spectroscopic (CD and NMR) methods. Analysis of separated fruit parts, i.e., the fruit wall and embryo, demonstrated the specific accumulation of arctiin, since it was exclusively found in the embryo. Arctiin in the embryo samples (71.5 mg/g) was found to be quantitatively converted into arctigenin (50.7 mg/g) by endogenous enzymatic hydrolysis, resulting in one of the highest arctigenin-containing plant tissues reported to date and allowing the selective isolation of arctigenin by our recently reported three-step isolation method. The absolute configuration of the isolated arctigenin was determined to be (-)-(8 R,8′ R). Conformational analysis of arctigenin was also performed, resulting in three major low energy conformations.

Comparison of the low energy conformations of an oncogenic and a non-oncogenic p21 protein, neither of which binds GTP or GDP

1994 ◽  
Vol 13 (2) ◽  
pp. 237-251 ◽  
Author(s):  
Adam Liwo ◽  
Kenneth D. Gibson ◽  
Harold A. Scheraga ◽  
Paul W. Brandt-Rauf ◽  
Regina Monaco ◽  
...  
Keyword(s):  
Low Energy ◽  
P21 Protein ◽  
Low Energy Conformations

The Low-Energy Conformations of Gonadotropin-Releasing Hormone in Aqueous Solution

2014 ◽  
Vol 33 (6) ◽  
pp. 565-574 ◽  
Author(s):  
Matthew R. Pincus ◽  
Jannie Woo ◽  
Regina Monaco ◽  
Jack Lubowsky ◽  
Matthew J. Avitable ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Gonadotropin Releasing Hormone ◽  
Low Energy ◽  
Releasing Hormone ◽  
Low Energy Conformations

Quantum Mechanics and Molecular Mechanics Studies of the Low-Energy Conformations of 9-Crown-3

1997 ◽  
Vol 101 (10) ◽  
pp. 1920-1926 ◽  
Author(s):  
Wayne P. Anderson ◽  
Philip Behm ◽  
Timothy M. Glennon ◽  
Michael C. Zerner
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Low Energy ◽  
Low Energy Conformations
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