Effect of helix length on the stability of the lac repressor antiparallel coiled coil

Biopolymers ◽  
2015 ◽  
Vol 104 (4) ◽  
pp. 395-404 ◽  
Author(s):  
Wheaton Little ◽  
James P. Robblee ◽  
Caroline L. Dahlberg ◽  
Bashkim Kokona ◽  
Robert Fairman
Keyword(s):  
Coiled Coil ◽  
Lac Repressor ◽  
The Stability ◽  
Antiparallel Coiled Coil

scholarly journals Antiparallel Coiled-Coil Interactions Mediate the Homodimerization of the DNA Damage-Repair Protein PALB2

Biochemistry ◽  
2018 ◽  
Vol 57 (47) ◽  
pp. 6581-6591 ◽  
Author(s):  
Fei Song ◽  
Minxing Li ◽  
Gaohua Liu ◽  
G.V.T. Swapna ◽  
Nourhan S. Daigham ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Damage Repair ◽  
Coiled Coil ◽  
Damage Repair ◽  
Repair Protein ◽  
Antiparallel Coiled Coil

Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide

2005 ◽  
Vol 3 (7) ◽  
pp. 1189 ◽  
Author(s):  
Kevin Pagel ◽  
Karsten Seeger ◽  
Bettina Seiwert ◽  
Alessandra VillaCurrent address: J. W. Goethe ◽  
Alan E. Mark ◽  
...  
Keyword(s):  
De Novo ◽  
Coiled Coil ◽  
Antiparallel Coiled Coil

Electrostatics and Self-Contact in an Elastic Rod Approximation for DNA

2010 ◽  
Vol 6 (1) ◽  
Author(s):  
Todd D. Lillian ◽  
N. C. Perkins
Keyword(s):  
Electrostatic Interactions ◽  
Regulatory Protein ◽  
Dna Supercoiling ◽  
Lac Repressor ◽  
Dna Looping ◽  
Elastic Rod ◽  
Storage And Retrieval ◽  
Cellular Processes ◽  
The Stability ◽  
Straight Rod

Deoxyribonucleic acid (DNA) is an essential molecule that enables the storage and retrieval of genetic information. In its role during cellular processes, this long flexible molecule is significantly bent and twisted. Previously, we developed an elastodynamic rod approximation to study DNA deformed into a loop by a gene regulatory protein (lac repressor) and predicted the energetics and topology of the loops. Although adequate for DNA looping, our model neglected electrostatic interactions, which are essential when considering processes that result in highly supercoiled DNA including plectonemes. Herein, we extend the rod approximation to account for electrostatic interactions and present strategies that improve computational efficiency. Our calculations for the stability for a circularly bent rod and for an initially straight rod compare favorably to existing equilibrium models. With this new capability, we are now well-positioned to study the dynamics of transcription and other dynamic processes that result in DNA supercoiling.

Electrostatics and Self Contact in an Elastic Rod Approximation for DNA

2009 ◽  
Author(s):  
Todd D. Lillian ◽  
N. C. Perkins
Keyword(s):  
Electrostatic Interactions ◽  
Regulatory Protein ◽  
Dna Supercoiling ◽  
Lac Repressor ◽  
Dna Looping ◽  
Elastic Rod ◽  
Storage And Retrieval ◽  
Cellular Processes ◽  
The Stability ◽  
Straight Rod

DNA is a life-sustaining molecule that enables the storage and retrieval of genetic information. In its role during essential cellular processes, this long flexible molecule is significantly bent and twisted. Previously, we developed an elasto-dynamic rod approximation to study DNA deformed into a loop by a gene regulatory protein (lac repressor) and predicted the energetics and topology of the loops. Although adequate for DNA looping, our model neglected electrostatic interactions which are essential when considering processes that result in highly super-coiled DNA including plectonemes. Herein we extend the rod approximation to account for electrostatic interactions and present strategies that improve computational efficiency. Our calculations for the stability for a circularly bent rod and for an initially straight rod compare favorably to existing equilibrium models. With this new capability, we are now well-positioned to study the dynamics of transcription and other dynamic processes that result in DNA supercoiling.

scholarly journals Determination of the Multimerization State of the Hepatitis Delta Virus Antigens In Vivo

2003 ◽  
Vol 77 (19) ◽  
pp. 10314-10326 ◽  
Author(s):  
Cromwell T. Cornillez-Ty ◽  
David W. Lazinski
Keyword(s):  
Crystal Structure ◽  
Hepatitis Delta Virus ◽  
Coiled Coil ◽  
Proper Function ◽  
Hepatitis Delta ◽  
Amino Terminal ◽  
Delta Antigen ◽  
Antiparallel Coiled Coil ◽  
Delta Virus

ABSTRACT Hepatitis delta virus expresses two essential proteins, the small and large delta antigens, and both are required for viral propagation. Proper function of each protein depends on the presence of a common amino-terminal multimerization domain. A crystal structure, solved using a peptide fragment that contained residues 12 to 60, depicts the formation of an octameric ring composed of antiparallel coiled-coil dimers. Because this crystal structure was solved for only a fragment of the delta antigens, it is unknown whether octamers actually form in vivo at physiological protein concentrations and in the context of either intact delta antigen. To test the relevance of the octameric structure, we developed a new method to probe coiled-coil structures in vivo. We generated a panel of mutants containing cysteine substitutions at strategic locations within the predicted monomer-monomer interface and the dimer-dimer interface. Since the small delta antigen contains no cysteine residues, treatment of cell extracts with a mild oxidizing reagent was expected to induce disulfide bond formation only when the appropriate pairs of cysteine substitution mutants were coexpressed. We indeed found that, in vivo, both the small and large delta antigens assembled as antiparallel coiled-coil dimers. Likewise, we found that both proteins could assume an octameric quaternary structure in vivo. Finally, during the course of these experiments, we found that unprenylated large delta antigen molecules could be disulfide cross-linked via the sole cysteine residue located within the carboxy terminus. Therefore, in vivo, the C terminus likely provides an additional site of protein-protein interaction for the large delta antigen.

scholarly journals Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes

2010 ◽  
Vol 191 (6) ◽  
pp. 1127-1139 ◽  
Author(s):  
Sajjan Koirala ◽  
Huyen T. Bui ◽  
Heidi L. Schubert ◽  
Debra M. Eckert ◽  
Christopher P. Hill ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Crystal Structures ◽  
Binding Sites ◽  
Mitochondrial Fission ◽  
Coiled Coil ◽  
Adaptor Proteins ◽  
Molecular Architecture ◽  
Cellular Membranes ◽  
Membrane Scission ◽  
Antiparallel Coiled Coil

Recruitment and assembly of some dynamin-related guanosine triphosphatases depends on adaptor proteins restricted to distinct cellular membranes. The yeast Mdv1 adaptor localizes to mitochondria by binding to the membrane protein Fis1. Subsequent Mdv1 binding to the mitochondrial dynamin Dnm1 stimulates Dnm1 assembly into spirals, which encircle and divide the mitochondrial compartment. In this study, we report that dimeric Mdv1 is joined at its center by a 92-Å antiparallel coiled coil (CC). Modeling of the Fis1–Mdv1 complex using available crystal structures suggests that the Mdv1 CC lies parallel to the bilayer with N termini at opposite ends bound to Fis1 and C-terminal β-propeller domains (Dnm1-binding sites) extending into the cytoplasm. A CC length of appropriate length and sequence is necessary for optimal Mdv1 interaction with Fis1 and Dnm1 and is important for proper Dnm1 assembly before membrane scission. Our results provide a framework for understanding how adaptors act as scaffolds to orient and stabilize the assembly of dynamins on membranes.

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