scholarly journals Activation mechanism of Drosophila cryptochrome through an allosteric switch

2021 ◽  
Vol 7 (25) ◽  
pp. eabg3815
Author(s):  
Yingjie Wang ◽  
Gianluigi Veglia ◽  
Dongping Zhong ◽  
Jiali Gao
Keyword(s):  
Computational Models ◽  
Dynamic Network ◽  
Salt Bridge ◽  
Structural Features ◽  
Activation Mechanism ◽  
Radius Of Gyration ◽  
Activation Process ◽  
Amino Terminal ◽  
Global Dynamic ◽  
Carboxyl Terminal

Cryptochromes are signaling proteins activated by photoexcitation of the flavin adenine dinucleotide (FAD) cofactor. Although extensive research has been performed, the mechanism for this allosteric process is still unknown. We constructed three computational models, corresponding to different redox states of the FAD cofactor in Drosophila cryptochrome (dCRY). Analyses of the dynamics trajectories reveal that the activation process occurs in the semiquinone state FAD−●, resulting from excited-state electron transfer. The Arg381-Asp410 salt bridge acts as an allosteric switch, regulated by the change in the redox state of FAD. In turn, Asp410 forms new hydrogen bonds, connecting allosteric networks of the amino-terminal and carboxyl-terminal domains initially separated in the resting state. The expansion to a global dynamic network leads to enhanced protein fluctuations, an increase in the radius of gyration, and the expulsion of the carboxyl-terminal tail. These structural features are in accord with mutations and spectroscopic experiments.

scholarly journals Signals and structural features involved in integral membrane protein targeting to the inner nuclear membrane.

1995 ◽  
Vol 130 (1) ◽  
pp. 15-27 ◽  
Author(s):  
B Soullam ◽  
H J Worman
Keyword(s):  
Membrane Protein ◽  
Nuclear Membrane ◽  
Structural Features ◽  
Inner Nuclear Membrane ◽  
Amino Terminal ◽  
Terminal Domain ◽  
Integral Protein ◽  
Carboxyl Terminal Domain ◽  
Carboxyl Terminal ◽  
Amino Terminal Domain

We have examined transfected cells by immunofluorescence microscopy to determine the signals and structural features required for the targeting of integral membrane proteins to the inner nuclear membrane. Lamin B receptor (LBR) is a resident protein of the nuclear envelope inner membrane that has a nucleoplasmic, amino-terminal domain and a carboxyl-terminal domain with eight putative transmembrane segments. The amino-terminal domain of LBR can target both a cytosolic protein to the nucleus and a type II integral protein to the inner nuclear membrane. Neither a nuclear localization signal (NLS) of a soluble protein, nor full-length histone H1, can target an integral protein to the inner nuclear membrane although they can target cytosolic proteins to the nucleus. The addition of an NLS to a protein normally located in the inner nuclear membrane, however, does not inhibit its targeting. When the amino-terminal domain of LBR is increased in size from approximately 22.5 to approximately 70 kD, the chimeric protein cannot reach the inner nuclear membrane. The carboxyl-terminal domain of LBR, separated from the amino-terminal domain, also concentrates in the inner nuclear membrane, demonstrating two nonoverlapping targeting signals in this protein. Signals and structural features required for the inner nuclear membrane targeting of proteins are distinct from those involved in targeting soluble polypeptides to the nucleoplasm. The structure of the nucleocytoplasmic domain of an inner nuclear membrane protein also influences targeting, possibly because of size constraints dictated by the lateral channels of the nuclear pore complexes.

scholarly journals Elucidating the Molecular Basis of pH Activation of an Engineered Mechanosensitive Channel

2019 ◽  
Author(s):  
Kalyan Immadisetty ◽  
Adithya Polasa ◽  
Reid Shelton ◽  
Mahmoud Moradi
Keyword(s):  
Mechanical Energy ◽  
Salt Bridge ◽  
Md Simulations ◽  
Pressure Profile ◽  
Chemical Signals ◽  
Activation Mechanism ◽  
Activation Process ◽  
Ph Change ◽  
Non Equilibrium Molecular Dynamics ◽  
First Time

AbstractMechanosensitive (MS) channels detect and respond to changes in the pressure profile of cellular membranes and transduce the mechanical energy into electrical and/or chemical signals. By re-engineering, however, the activation of some MS channels can be triggered by chemical signals such as pH change. Here, for the first time, we have elucidated, at an atomic level, the activation mechanism of an engineered MscL channel in response to the pH changes of the environment through a combination of equilibrium and non-equilibrium molecular dynamics (MD) simulations. The key highlights of our proposed activation mechanism are that: (1) periplasmic loops play a key role in activation, (2) loss of various hydrogen bonding and salt bridge interactions in the engineered MscL channel causes the opening of the channel, and (3) the most significant interactions lost during the activation process are those between the transmembrane (TM) helices 1 and 2 (TM1 and TM2). The orientation-based method in this work for generating and optimizing an open model of engineered MscL is a promising method for generating unknown states of proteins and for studying the activation processes in ion channels. This work facilitates the studies aimed at designing pH-triggered drug delivery liposomes (DDL), which embed MscL as a nanovalve.

The Reactive Formation of Diblock Copolymer at a Polymer/Polymer Interface and its Effect on Interfacial Structure

2000 ◽  
Vol 629 ◽  
Author(s):  
Jonathan S. Schulze ◽  
Timothy P. Lodge ◽  
Christopher W. Macosko
Keyword(s):  
Molecular Weight ◽  
Interfacial Structure ◽  
Root Mean Square Roughness ◽  
Radius Of Gyration ◽  
Interfacial Region ◽  
Force Microscopy ◽  
Amino Terminal ◽  
Polymer Interface ◽  
Atomic Force ◽  
Time Required

ABSTRACTThe reaction of perdeuterated amino-terminal polystyrene (dPS-NH2) with anhydrideterminal poly(methyl methacrylate) (PMMA-anh) at a PS/PMMA interface has been observed with forward recoil spectrometry (FRES). Bilayer samples were constructed by placing thin films of PS containing ∼8.5 wt % dPS-NH2 on a PMMA-anh layer. Significant reaction was observed only after annealing the samples at 174°C for several hours, a time scale at least two orders of magnitude greater than the time required for the dPS-NH2 chains to diffuse through the bulk PS layer. The topography of the interfacial region as copolymer formed was measured using atomic force microscopy (AFM). Roughening of the PS/PMMA interface was observed to varying degrees in all annealed samples. Furthermore, the extent of this roughening was found to depend on the PS matrix molecular weight. Reaction in the samples with a high molecular weight PS matrix resulted in a root mean square roughness approximately equal to the radius of gyration Rg of the copolymer. However, approximately twice as much roughening was observed in the low molecular weight PS matrix. This study reveals how the molecular weight of one of the phases can affect the rate of reaction at a polymer/polymer interface.

scholarly journals Evolution of the hedgehog Gene Family

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 965-972 ◽  
Author(s):  
Sudhir Kumar ◽  
Kristi A Balczarek ◽  
Zhi-Chun Lai
Keyword(s):  
Intercellular Communication ◽  
Short Range ◽  
Gene Duplications ◽  
Future Directions ◽  
Amino Terminal ◽  
Terminal Fragment ◽  
Carboxyl Terminal ◽  
Multicellular Organisms ◽  
Amino Terminal Fragment

Abstract Effective intercellular communication is an important feature in the development of multicellular organisms. Secreted hedgehog (hh) protein is essential for both long- and short-range cellular signaling required for body pattern formation in animals. In a molecular evolutionary study, we find that the vertebrate homologs of the Drosophila hh gene arose by two gene duplications: the first gave rise to Desert hh, whereas the second produced the Indian and Sonic hh genes. Both duplications occurred before the emergence of vertebrates and probably before the evolution of chordates. The amino-terminal fragment of the hh precursor, crucial in long- and short-range intercellular communication, evolves two to four times slower than the carboxyl-terminal fragment in both Drosophila hh and its vertebrate homologues, suggesting conservation of mechanism of hh action in animals. A majority of amino acid substitutions in the amino- and carboxyl-terminal fragments are conservative, but the carboxyl-terminal domain has undergone extensive insertion-deletion events while maintaining its autocleavage protease activity. Our results point to similarity of evolutionary constraints among sites of Drosophila and vertebrate hh homologs and suggest some future directions for understanding the role of hh genes in the evolution of developmental complexity in animals.

scholarly journals p190 RhoGAP, the major RasGAP-associated protein, binds GTP directly.

1994 ◽  
Vol 14 (11) ◽  
pp. 7173-7181 ◽  
Author(s):  
R Foster ◽  
K Q Hu ◽  
D A Shaywitz ◽  
J Settleman
Keyword(s):  
Structural Features ◽  
Cellular Protein ◽  
Small Gtpases ◽  
Sequence Motifs ◽  
Amino Terminal ◽  
Terminal Domain ◽  
Gtp Binding ◽  
Guanine Nucleotide Binding ◽  
Complex Forms ◽  
Carboxy Terminal

In mitogenically stimulated cells, a specific complex forms between the Ras GTPase-activating protein (RasGAP) and the cellular protein p190. We have previously reported that p190 contains a carboxy-terminal domain that functions as a GAP for the Rho family GTPases. Thus, the RasGAP-p190 complex may serve to couple Ras- and Rho-mediated signalling pathways. In addition to its RhoGAP domain, p190 contains an amino-terminal domain that contains sequence motifs found in all known GTPases. Here, we report that p190 binds GTP and GDP through this conserved domain and that the structural requirements for binding are similar to those seen with other GTPases. While the purified protein is unable to hydrolyze GTP, we detect an activity in cell lysates that can promote GTP hydrolysis by p190. A mutated form of p190 that fails to bind nucleotide retains its RasGAP binding and RhoGAP activities, indicating that GTP binding by p190 is not required for these functions. The sequence of p190 in the GTP-binding domain, which shares structural features with both the Ras-like small GTPases and the larger G proteins, suggests that this protein defines a novel class of guanine nucleotide-binding proteins.

scholarly journals Identification and characterization of a novel cytoskeleton-associated pp60src substrate.

1991 ◽  
Vol 11 (10) ◽  
pp. 5113-5124 ◽  
Author(s):  
H Wu ◽  
A B Reynolds ◽  
S B Kanner ◽  
R R Vines ◽  
J T Parsons
Keyword(s):  
Cell Structure ◽  
Transformed Cells ◽  
Cdna Clones ◽  
Amino Terminal ◽  
Multidomain Structure ◽  
Striking Change ◽  
Carboxyl Terminal ◽  
Amino Terminal Domain ◽  
Related Proteins

Transformation of cells by the src oncogene results in elevated tyrosine phosphorylation of two related proteins, p80 and p85 (p80/85). Immunostaining with specific monoclonal antibodies revealed a striking change of subcellular localization of p80/85 in src-transformed cells. p80/85 colocalizes with F-actin in peripheral extensions of normal cells and rosettes (podosomes) of src-transformed cells. Sequence analysis of cDNA clones encoding p80/85 revealed an amino-terminal domain composed of six copies of a direct tandem repeat, each repeat containing 37 amino acids, a carboxyl-terminal SH3 domain, and an interdomain region composed of a highly charged acidic region and a region rich in proline, serine, and threonine. The multidomain structure of p80/85 and its colocalization with F-actin in normal and src-transformed cells suggest that these proteins may associate with components of the cytoskeleton and contribute to organization of cell structure.

Determination of amino- and carboxyl-terminal sequences of guinea pig liver transglutaminase: evidence for amino-terminal processing

Biochemistry ◽  
1989 ◽  
Vol 28 (5) ◽  
pp. 2344-2348 ◽  
Author(s):  
Koji Ikura ◽  
Hiroyuki Yokota ◽  
Ryuzo Sasaki ◽  
Hideo Chiba
Keyword(s):  
Guinea Pig ◽  
Pig Liver ◽  
Amino Terminal ◽  
Carboxyl Terminal ◽  
Guinea Pig Liver

scholarly journals Interactions between Integrase and Excisionase in the Phage Lambda Excisive Nucleoprotein Complex

2002 ◽  
Vol 184 (18) ◽  
pp. 5200-5203 ◽  
Author(s):  
Eun Hee Cho ◽  
Richard I. Gumport ◽  
Jeffrey F. Gardner
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Mobility Shift ◽  
Host Chromosome ◽  
Amino Terminal ◽  
Nucleoprotein Complex ◽  
Carboxyl Terminal ◽  
Α Helix ◽  
Gel Mobility Shift ◽  
Amino Terminal Domain

ABSTRACT Bacteriophage lambda site-specific recombination comprises two overall reactions, integration into and excision from the host chromosome. Lambda integrase (Int) carries out both reactions. During excision, excisionase (Xis) helps Int to bind DNA and introduces a bend in the DNA that facilitates formation of the proper excisive nucleoprotein complex. The carboxyl-terminal α-helix of Xis is thought to interact with Int through direct protein-protein interactions. In this study, we used gel mobility shift assays to show that the amino-terminal domain of Int maintained cooperative interactions with Xis. This finding indicates that the amino-terminal arm-type DNA binding domain of Int interacts with Xis.

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