Program PROTEUS for adding hydrogens to a protein structure and electrostatic field across carotenoids in light harvesting complexes and reaction centers from bacterial sources.
Item
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Title
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Program PROTEUS for adding hydrogens to a protein structure and electrostatic field across carotenoids in light harvesting complexes and reaction centers from bacterial sources.
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Identifier
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AAI9997103
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identifier
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9997103
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Creator
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Lipovaca, Samir.
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Contributor
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Adviser: Marilyn R. Gunner
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Date
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2001
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Language
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English
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Publisher
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City University of New York.
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Subject
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Physics, Condensed Matter
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Abstract
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The hydrogen construction method presented in the program PROTEUS treats hydrogens depending on their torsional degrees of freedom. The positions of hydrogens with restricted torsional degrees of freedom are completely determined by the heavy atoms positions in the structure. The hydroxyl and water hydrogens are the only hydrogens that PROTEUS accepts as movable hydrogens (having rotational degrees of freedom). Their positions are determined by the interactions with neighboring atoms. PROTEUS interaction energy corresponds to a view that the hydrogen bond is affected, besides electrostatic effects and steric constraints of neighboring groups, by an inherent energy barrier that opposes free rotation of the hydroxyl hydrogen. For the water hydrogens that barrier is zero. The hydroxyl and water hydrogens are minimized within a short distance using the Threshold Accepting (TA) energy minimization method. PROTEUS can provide reasonable positions of movable hydrogens and a good initial protein structure for further investigations.;We applied the program PROTEUS to place hydrogens in several resolved three-dimensional crystal structures of light harvesting complexes (LHCs) and reaction centers (RCs) from bacterial sources. Using program DelPhi we calculated the local electrostatic field across carotenoid generated by the protein's charges. In each structure we identified amino acids responsible for the field. Much of the field is generated by the charged residues. There are different ways that a RC or LHC uses charged residues. A nearby dipole consisting of the charged residues which are ionized in the physiological pH range (like Arg-Asp), is often used. Clusters of charged residues or scattered isolated charged residues around the carotenoid molecule also contribute. The polarizable field is not necessarily along the carotenoid molecule principal axis. For soluble LHCs the contribution of polar residues to the field cannot be neglected. Our calculations indicate an important relation between the field and the protein's overall structure: the minimum value of the field arises from the backbone dipoles. In contrast to the charged residues, hydroxyl and water dipoles are responsible for a fine tuning of the field in a response to the protein's environment.
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Type
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dissertation
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Source
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PQT Legacy CUNY.xlsx
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degree
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Ph.D.
