Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA.

08:00 EDT 10th August 2017 | BioPortfolio

Summary of "Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA."

The starting point of many fundamental biological processes is associated with protein molecules finding and recognizing specific sites on DNA. However, despite a large number of experimental and theoretical studies on protein search for targets on DNA, many molecular aspects of underlying mechanisms are still not well understood. Experiments show that proteins bound to DNA can switch between slow recognition and fast search conformations. However, from a theoretical point of view, such conformational transitions should slow down the protein search for specific sites on DNA, in contrast to available experimental observations. In addition, experiments indicate that the nucleotide composition near the target site is more symmetrically homogeneous, leading to stronger effective interactions between proteins and DNA at these locations. But, as has been shown theoretically, this should also make the search less efficient, that is not observed. We propose a possible resolution of these problems by suggesting that conformational transitions occur only within a segment around the target where stronger interactions between proteins and DNA are observed. Two theoretical methods, based on continuum and discrete-state stochastic calculations, are developed, allowing us to obtain a comprehensive dynamic description for the protein search process in this system. The existence of an optimal length of the conformational transition zone with the shortest mean search time is predicted.


Journal Details

This article was published in the following journal.

Name: The journal of physical chemistry letters
ISSN: 1948-7185


DeepDyve research library

PubMed Articles [26217 Associated PubMed Articles listed on BioPortfolio]

Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model.

Conformational entropy is expected to contribute significantly to the thermodynamics of structural transitions in intrinsically disordered proteins or regions in response to protein/ligand binding, po...

Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA.

The amplitude of thermodynamic fluctuations in biological macromolecules determines their conformational behavior, dimensions, nature of phase transitions and effectively their specificity and affinit...

Oxygenation of the Immature Infant: A Commentary and Recommendations for Oxygen Saturation Targets and Alarm Limits.

For 70 years, there has been a search for the optimal oxygenation of premature infants. In spite of the lack of evidence, guidelines have successively reduced oxygenation targets during these years.

Structural Basis of Protein Kinase Cα Regulation by the C-Terminal Tail.

Protein kinase C (PKC) isoenzymes are multi-modular proteins activated at the membrane surface to regulate signal transduction processes. When activated by second messengers, PKC undergoes a drastic c...

Conformational Ensemble and Biological Role of the TCTP Intrinsically Disordered Region: Influence of Calcium and Phosphorylation.

The translationally controlled tumor protein (TCTP) is a multifunctional protein that may interact with many other bio-mole-cules, including itself. The experimental determinations of TCTP structure r...

Clinical Trials [6399 Associated Clinical Trials listed on BioPortfolio]

: TRANSITION: An Observational Study of Transition From Lumacaftor/Ivacaftor to Tezacaftor/Ivacaftor (Tez/Iva)

This study is a single center study of clinical and laboratory outcomes in patients ≥ 12 who transition from use of Orkambi to tez/iva. Clinical and laboratory measurements will be measu...

A Pilot Trial of Atorvastatin in Tumor Protein 53 (p53) -Mutant and p53 Wild-Type Malignancies

This is a window-of-opportunity trial to determine if atorvastatin given for 1 to 4 weeks at a dose of 80 milligrams per day (mg/day) is sufficient to decrease the level of conformational ...

Personalized Non-invasive Neuromodulation by rTMS for Chronic and Treatment Resistant Catatonia

Investigators hypothesize that personalizing rTMS targets using functional MRI will allow to improve symptoms of patients suffering from chronic catatonia.

Improving Health Care Transition for Youth With Special Needs

Special opportunities exist in vulnerable populations with chronic conditions to better understand what life course factors can facilitate attainment of optimal health and development. One...

Automated Youth-To-Adult Transition Planning Using Health Information ...

This study seeks to automate the process of youth to adult transition using an existing computerized decision support system in primary care. Subjects will complete the TRAQ readiness ques...

Medical and Biotech [MESH] Definitions

Protein domains that are enriched in PROLINE. The cyclical nature of proline causes the peptide bonds it forms to have a limited degree of conformational mobility. Therefore the presence of multiple prolines in close proximity to each other can convey a distinct conformational arrangement to a peptide chain.

Conformational transitions of the shape of a protein to various unfolded states.

Conformational transitions of a protein from unfolded states to a more folded state.

A poly(A) binding protein that is involved in promoting the extension of the poly A tails of MRNA. The protein requires a minimum of ten ADENOSINE nucleotides in order for binding to mRNA. Once bound it works in conjunction with CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR to stimulate the rate of poly A synthesis by POLY A POLYMERASE. Once poly-A tails reach around 250 nucleotides in length poly(A) binding protein II no longer stimulates POLYADENYLATION. Mutations within a GCG repeat region in the gene for poly(A) binding protein II have been shown to cause the disease MUSCULAR DYSTROPHY, OCULOPHARYNGEAL.

An analytical method for detecting and measuring FLUORESCENCE in compounds or targets such as cells, proteins, or nucleotides, or targets previously labeled with FLUORESCENCE AGENTS.

Quick Search


DeepDyve research library

Relevant Topics

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Biological Therapy
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...

Searches Linking to this Article