*  Alternate Conformations
The following examples show how to set up alternate conformations for structure factor calculations as well as for empirical energy calculations. The first step is to append the alternate conformations to the current molecular structure file. In this particular case, one wants to generate alternate conformations for the side chains of residues 1 and 7. alternate.inp Now one has to go to the graphics and move the alternate conformations into the correct positions. In subsequent protocols, one has to insert the following statement after reading the molecular structure file ...
*  The contribution of conformational adjustments and long-range electrostatic forces to the CD2/CD58 interaction | Davis Lab...
CD2 is a T cell surface molecule that enhances T and natural killer cell function by binding its ligands CD58 (humans) and CD48 (rodents) on antigen-presenting or target cells. Here we show that the CD2/CD58 interaction is enthalpically driven and accompanied by unfavorable entropic changes. Taken together with structural studies, this indicates that binding is accompanied by energetically significant conformational adjustments. Despite having a highly charged binding interface, neither the affinity nor the rate constants of the CD2/CD58 interaction were affected by changes in ionic strength, indicating that long-range electrostatic forces make no net contribution to binding.. ...
*  Conformation of stereoregular PMMA in solutions during the temperature induced conformational transition
The temperature induced conformational transition of stereoregular PMMA in diluted or semi-diluted solution was studied by viscometry, NMR and FT-IR. The conformational energies of polymer chains were calculated from infrared spectral subtraction by following the method described by O'Reilly and Mosher [O'Reilly JM, Mosher RA. Macromolecules, 14 (1981) 602; O'Reilly JM, Teegarden DM, Mosher RA. Macromolecules, 14 (1981) 1693]. The fraction of sequences containing gauche conformation that can be deduced shows a large increase during the conformational transition. This increase in the probability of gauche conformations accounts for an increase in the chain flexibility deduced from the decrease of the calculated characteristic ratio. The increment in the hydrodynamic volume of the chain in chloroform that occurs at the transition temperature can be correlated with an increase in the density of the polymer-solvent specific interactions. The range of ...
In contrast to micelles and bilayers, which are composed of aggregates of single and double chain amphphiles, proteins are covalent polymers of 20 different amino acids, which fold, to a first approximation, in a thermodynamically spontaneous process into a single unique conformation, theoretically at a global energy minimum. This section will investigate the possible conformations available to proteins, just as we studied the conformations of free fatty acids and acyl chains in lipid aggregates. The next section will discuss the actual processes of folding and of unfolding (denaturation), both in vitro and in vivo. The last will discuss the thermodynamics and intermolecular forces which stabilize the folded (or native) shape and the unfolded (or denatured state) of proteins, in a fashion similar to how we discussed micelle and bilayer stability.. Main Chain Conformations - Cis/Trans Peptide Bonds/ Ramachandran Plots Just as ...
*  DynDom - Protein Domain Motions
DynDom is a program that determines protein domains, hinge axes and amino acid residues involved in the hinge bending. It is fully automated.. You can use DynDom if you have two conformations of the same protein. These may be two X-ray structures, or structures generated using simulation techniques such as molecular dynamics or normal mode analysis.. The application of DynDom provides a view of the conformational change that is easily understood. The conformational change may be quite complicated in detail, but by using DynDom you can visualize it as involving the movement of domains as quasi-rigid bodies. The analysis of a conformational change in terms of domain movements only makes sense if the interdomain deformation is at least comparable to the intradomain deformation. You can use DynDom to assess this, but the results could be misleading if this is not the case.. DynDom allows you to visualize the domain motion in ...
*  Conformational equilibria and intrinsic affinities define integrin activation | The EMBO Journal
Integrins undergo large‐scale conformational changes (Springer & Dustin, 2012). In the bent‐closed (BC) conformation, the integrin ectodomain folds at knees in the α‐ and β‐subunits so that the head and upper legs associate with the lower legs (Fig 1A). In two extended states, the extended‐closed (EC) and extended‐open (EO) conformations, extension of the α‐ and β‐knees raises the headpiece above the lower legs on cell surfaces (Fig 1A). In transition from EC to EO, that is, headpiece opening, the ligand‐binding metal ion‐dependent adhesion site (MIDAS) in the β‐subunit βI domain rearranges. This reshaping of the ligand‐binding site is linked by α‐helix pistoning within the βI domain to swing of the hybrid domain away from the integrin α‐subunit (Fig 1A). Although the affinities of these states have not yet been measured, previous studies have correlated integrin adhesiveness and high affinity for ligand with the EO conformation (Takagi et al, 2002, 2003; ...
*  Pyrene: A Probe to Study Protein Conformation and Conformational Changes - pdf download
Pyrene: A Probe to Study Protein Conformation and Conformational Changes. . Download books free in pdf. Online library with books, university works and thousands of documents available to read online and download.
*  STIM1 couples to ORAI1 via an intramolecular transition into an extended conformation | The EMBO Journal
Here, we presented a STIM1‐derived conformational sensor that allowed for probing of intramolecular transitions within its cytosolic domains. This region of STIM1 switched from a tight into an extended conformation either by interaction with ORAI1 or via mutations introduced in the first or third putative coiled‐coil domain. These engineered STIM1 constructs with extended conformations exhibited an enhanced interaction with both wild‐type and the SCID‐linked R91W mutant ORAI1. The mutation‐induced extended STIM1 C‐terminal conformation reflects an intramolecular transition, which likely exposes the CAD/SOAR domain and promotes interaction of full‐length STIM1 with ORAI1, even in the absence of store depletion. We suggest that these mutant full‐length STIM1 proteins that interact with and constitutively activate ORAI1 channels imitate a physiological activated state, which mimics the conformational change that occurs in native STIM1 upon store depletion. The ...
*  Evolution of Cytokine Receptor Signaling | The Journal of Immunology
FIGURE 1. Coalescence of the CytoR signaling pathway. Schematic representation of the evolutionary history of individual CytoR signaling components is depicted in the outer hexagonal segments: Cyto (gray), CytoR (blue), JAK (green), STAT (brown), SHP (purple), SOCS (light orange), including a simplified tree of the key organismal groups considered. The domain architecture of each component within these groups is depicted, showing the accretion (purple arrows) and modification or de novo generation of protein domains into the archetypal topology (outlined). This coalesced into a functional CytoR signaling pathway in bilateria (central circle), in which Cyto binding to the CytoR causes conformational changes that initiate JAK activation and CytoR phosphorylation, creating docking sites for STAT. These are phosphorylated by JAK (blue arrow) and translocate to the nucleus (yellow arrow) to initiate transcription of target genes (green arrow) to mediate an appropriate response, ...
*  protein folding
Your question assumes that (1) a potential energy function can be described , and that (2) the 'normal' or functional conformation of a protein is one in , which the potential energy is at a global minimum. But neither of these is a , valid assumption. This I don't get. (1) Why shouldn't we be able to 'describe' the potential energy function, at least for some subspace of the conformational space. (2) I have argued before that we may never know for sure whether proteins attain their global minimum (without breaking bonds!) in their native fold. However, in almost every known case there is no reason whatsoever to assume that the Anfinsen hypothesis (proteins fold to their energy minimum) is not true. If you think this isn't the case, please explain why. , In particular, (2) is biologically meaningless, because a protein in its , global minimum would not be capable of assuming different conformations , without an external ...
*  Levels of protein structure and how they are affected by denaturation | Biology
Secondary structure this is the arrangement of amino acids in the localized areas of a protein molecule. These folding patterns are stabilized by hydrogen bonds. The main structures in this level are alpha helix structure and anti-parallel beta-pleated sheet. Although there are different periodic conformations, alpha and beta pleated sheets are the most stable. A protein or single polypeptide can be comprised of more than one secondary structure. Alpha-helix is a clockwise spiral with planar peptide bonds and a trans conformation. The amine groups for each of the peptide bond generally run upward at the same time parallel to the helix axis. Carboxyl group generally points in the upward direction. Beta-pleated sheets are made of extensive polypeptide chains. Their neighboring chains extend anti-parallel to one another. Each of their peptide bonds is planar and trans just like the ones for alpha-helix structure. The carboxyl and amine groups of the peptide bonds lie in the ...
*  DataSpace: Oligomers Designed to Study Conformational Changes of Nucleosome Bound DNA
This thesis can be viewed in person at the Mudd Manuscript Library. To order a copy complete the Senior Thesis Request Form. For more information contact mudd@princeton.edu ...
*  Questions about Conformations and Energy Profiles
Another example of the initial conformer affecting systematic results can be found by inspecting an 8 member carbon chain: "C1-C2-C3-C4-C5-C6-C7-C8". For illustrative purposes consider the central "C4-C5" bond as we rotate it 360 degrees; from -180 to 180 degrees. If one starts in the all 'trans' conformation, we find that as we rotate the "C4-C5" bond the final conformation of 360 degrees is identical to the initial at 0 degrees. However, if the initial conformation had a number of kinks in it, we might discover that at the 120 degree mark, the C1 and C8 ran into each other. To relieve this steric problem the other dihedral angles, will relax, likely changing by more than 100 degrees and falling into new energy wells. As we continue the coordinate driving of the central C4-C5 angle to trans (180), we might find that the final conformation is not the same as the initial conformation because these other dihedrals have changed ...
*  Obstructing conformational shifts in active proteins keeps therapeutic guarantee biologically. of - Role of adrenergic...
Obstructing conformational shifts in active proteins keeps therapeutic guarantee biologically. of taxol in vitro and in a xenograft style of lung tumor. Also the expected mode of actions of the energetic peptides was experimentally confirmed. Both peptides destined to their mother or father protein and their natural activity was abolished in the current presence of the peptides related towards the counterpart helices. These data demonstrate a uncharacterized way for rational style of proteins antagonists previously. displays the experimentally-derived get in touch with map of HIV-1 gp41 as extracted from PDB 1ENV. The helix-helix relationships can be recognized with a peak in the total value from the Fourier transform of the get in touch with map when used on the amount by rows (or individually by columns) from the relevant 21 × 21 operating submatrix. Fig. 1illustrates the Fourier transform related to the amount of rows representing the ...
*  Brookhaven Dental Associates Brookhaven, GA 30319 - YP.com
Get reviews, hours, directions, coupons and more for Brookhaven Dental Associates at 1407 Dresden Dr NE Ste 200, Brookhaven, GA. Search for other Dentists in Brookhaven on YP.com.
*  FCC Reveals Crucial Piece of TV Channel Repacking Method | TvTechnology
The FCC has quietly revealed what amounts to a core componenet of its methodology for repacking TV channels in the post-incentive auction spectrum band.
*  RCSB PDB - 1P1U: Crystal structure of the GluR2 ligand-binding core (S1S2J) L650T mutant in complex with AMPA ...
1P1U: Tuning activation of the AMPA-sensitive GluR2 ion channel by genetic adjustment of agonist-induced conformational changes.
*  Purdue e-Pubs - Society of Engineering Science 51st Annual Technical Meeting: Microtubule-driven conformational changes in...
The influence of the range of the involved geometric and material parameters, such as the available area for conformational changes, the bilayer thickness, the interaction energy between transmembrane domains and lipids, is largely explored. Bounds on the available conformations experienced by the transmebrane domains are also provided.
*  Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools...
Several programs (Catalyst, Confort, Flo99, MacroModel, and Omega) that are commonly used to generate conformational ensembles have been tested for their ability to reproduce bioactive conformations.
*  EMBOSS: aaindexextract
H CHOP780101 D Normalized frequency of beta-turn (Chou-Fasman, 1978a) R LIT:2004003a PMID:354496 A Chou, P.Y. and Fasman, G.D. T Empirical predictions of protein conformation J Ann. Rev. Biochem. 47, 251-276 (1978) C PALJ810106 0.977 TANS770110 0.956 CHAM830101 0.946 CHOP780203 0.940 CHOP780216 0.929 CHOP780210 0.921 ROBB760113 0.907 GEIM800108 0.899 QIAN880133 0.897 QIAN880132 0.896 LEVM780103 0.893 PRAM900104 0.891 LEVM780106 0.890 ROBB760108 0.887 BEGF750103 0.885 ISOY800103 0.885 CRAJ730103 0.882 GEIM800111 0.878 PALJ810105 0.868 ROBB760110 0.863 NAGK730103 0.827 QIAN880131 0.824 AURR980114 -0.803 BEGF750101 -0.803 QIAN880107 -0.809 KANM800103 -0.824 AURR980109 -0.837 SUEM840101 -0.845 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.66 0.95 1.56 1.46 1.19 0.98 0.74 1.56 0.95 0.47 0.59 1.01 0.60 0.60 1.52 1.43 0.96 0.96 1.14 0.50 // H CHOP780201 D Normalized frequency of alpha-helix (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of ...
*  Molecules | Free Full-Text | A Conformational Study of Flexible Cyclic Compounds (Hydrocarbon Rings of 9-12 Members)
We report here a conformational study of cyclic flexible compounds (rings with 9-12 members). Two methods of systematic search for the minima were used. The results were compared with those obtained using other exploratory methods.
*  Evolving L-Systems to Capture Protein Structure Native Conformations | SpringerLink
A protein is a linear chain of amino acids that folds into a unique functional structure, called its native state. In this state, proteins show repeated substructures like alpha helices and beta sheet
*  How many words make out of Conformational | Find all Anagrams
List of words make out of Conformational. All anagrams of Conformational. Words made after unscrambling Conformational. Scrabble Points. Puzzle Solver. Word Creation.