scholarly journals The Rosetta all-atom energy function for macromolecular modeling and design

2017 ◽  
Author(s):  
Rebecca F. Alford ◽  
Andrew Leaver-Fay ◽  
Jeliazko R. Jeliazkov ◽  
Matthew J. O'Meara ◽  
Frank P. DiMaio ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Energy Function ◽  
Crystal Structure Data ◽  
Structural Data ◽  
X Ray ◽  
The Past ◽  
Biomolecular Modeling ◽  
Macromolecular Modeling ◽  
Atom Energy

AbstractOver the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta’s success is the energy function: amodel parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, beta_nov15. Applying these concepts,we explain how to use Rosetta energies to identify and analyze the features of biomolecular models.Finally, we discuss the latest advances in the energy function that extend capabilities from soluble proteins to also include membrane proteins, peptides containing non-canonical amino acids, carbohydrates, nucleic acids, and other macromolecules.

On the Mechanism of Metabolic Reactions of Amino Acids Catalyzed by Vitamin B6 and Related Aldehydes

1994 ◽  
Vol 49 (9-10) ◽  
pp. 571-578 ◽  
Author(s):  
J. Sivý ◽  
V. Kettmann ◽  
J. Krätsmár-Šmogrovič
Keyword(s):  
Amino Acids ◽  
Quantum Chemical ◽  
Vitamin B6 ◽  
Structural Data ◽  
Alcohol Molecule ◽  
Vitamin B ◽  
Metal System ◽  
X Ray ◽  
Solvent Water ◽  
Metabolic Reactions

Abstract The crystal structure of [(N-salicylidene-ᴅ,ʟ-glutamato)(pyridine)]copper(II), a model for vitamin B6-amino acid-related metal complexes, has been determined by an X-ray analysis. A close examination of the structural data on this and other related complexes combined with quantum-chemical (INDO/2) calculations enabled us to make a clear distinction between two mechanisms proposed earlier for metabolic reactions of amino acids catalyzed by the vitamin B6 (or salicylaldehyde)-metal system. The results are consistent with a transient formation of a carbinolamine species resulting from the addition of a solvent water or alcohol molecule to the Schiff base double bond, thus supporting the mechanism of the catalysis as proposed by Gillard and Wootton.

Synthesis and Crystal Structure Determination of Cyclosporin H

2000 ◽  
Vol 65 (8) ◽  
pp. 1317-1328 ◽  
Author(s):  
Alexandr Jegorov ◽  
Ladislav Cvak ◽  
Aleš Husek ◽  
Petr Šimek ◽  
Anna Heydová ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Synthesis And Crystal Structure ◽  
X Ray ◽  
Acid Catalyzed ◽  
Products Of Reaction ◽  
Cyclosporin H

Acid-catalyzed degradation of cyclosporin A was studied in various solvents and products of reaction were monitored by HPLC. Identification of amino acids and their chirality were determined after hydrolysis and derivatization by GC-MS. Cyclosporin H was isolated as the principal product and its structure was determined by X-ray diffraction: Cyclosporin H- diethyl ether-water (1 : 0.5 : 1) crystallizes in the monoclinic space group I2 with a = 12.338(2) Å, b = 18.963(2) Å, c = 34.074(3) Å, β = 96.47(2)°, Z = 4, and V = 7 921.4(17) Å3.

Are gamma amino acids promising tools of crystal engineering? – Multicomponent crystals of baclofen

CrystEngComm ◽  
2015 ◽  
Vol 17 (43) ◽  
pp. 8264-8272 ◽  
Author(s):  
Nikoletta B. Báthori ◽  
Ornella E. Y. Kilinkissa
Keyword(s):  
Crystal Structure ◽  
Thermal Analysis ◽  
Amino Acids ◽  
Crystal Engineering ◽  
Sulfonic Acid ◽  
Dicarboxylic Acids ◽  
Monocarboxylic Acids ◽  
X Ray ◽  
Toluene Sulfonic Acid

The crystal structure, thermal analysis and powder X-ray analysis of the multicomponent crystals formed between baclofen and selected monocarboxylic acids, dicarboxylic acids and p-toluene sulfonic acid are presented.

scholarly journals Redetermination of ammonium metavanadate

IUCrData ◽  
2018 ◽  
Vol 3 (8) ◽  
Author(s):  
Aarón Pérez-Benítez ◽  
Sylvain Bernès
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Solid State ◽  
Single Crystal ◽  
Structural Data ◽  
Ammonium Cation ◽  
Ammonium Metavanadate ◽  
Starting Material ◽  
X Ray ◽  
Hydrogen Bonding Interactions

The crystal structure of ammonium metavanadate, NH4VO3, a compound widely used as a starting material for the synthesis of vanadium and polyoxidovanadate compounds, had been determined twice using single-crystal X-ray data [Syneček & Hanic (1954). Czech. J. Phys. 4, 120–129 (Weissenberg data); Hawthorne & Calvo (1977). J. Solid State Chem. 22, 157–170 (four-circle diffractometer data)]. Its structure is now redetermined at higher resolution using Ag Kα radiation, and the result is compared with the former refinements. Structural data for the polymeric [VO3]∞ chain remain unchanged, while more accurate parameters are obtained for the ammonium cation, improving the description of hydrogen-bonding interactions in the crystal structure.

scholarly journals Crystal structure of glycosyltrehalose synthase fromSulfolobus shibataeDSM5389

2018 ◽  
Vol 74 (11) ◽  
pp. 741-746
Author(s):  
Nobuo Okazaki ◽  
Michael Blaber ◽  
Ryota Kuroki ◽  
Taro Tamada
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Catalytic Mechanism ◽  
Catalytic Domain ◽  
Structural Basis ◽  
Hyperthermophilic Archaeon ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sulfolobus Shibatae ◽  
Glucosidic Bond

Glycosyltrehalose synthase (GTSase) converts the glucosidic bond between the last two glucose residues of amylose from an α-1,4 bond to an α-1,1 bond, generating a nonreducing glycosyl trehaloside, in the first step of the biosynthesis of trehalose. To better understand the structural basis of the catalytic mechanism, the crystal structure of GTSase from the hyperthermophilic archaeonSulfolobus shibataeDSM5389 (5389-GTSase) has been determined to 2.4 Å resolution by X-ray crystallography. The structure of 5389-GTSase can be divided into five domains. The central domain contains the (β/α)8-barrel fold that is conserved as the catalytic domain in the α-amylase family. Three invariant catalytic carboxylic amino acids in the α-amylase family are also found in GTSase at positions Asp241, Glu269 and Asp460 in the catalytic domain. The shape of the catalytic cavity and the pocket size at the bottom of the cavity correspond to the intramolecular transglycosylation mechanism proposed from previous enzymatic studies.

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