Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements.

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. Abstract Text:

BACKGROUND: Since experimental determination of protein folding pathways remains difficult, computational techniques are often used to simulate protein folding. Most current techniques to predict protein folding pathways are computationally intensive and are suitable only for small proteins. RESULTS: By assuming that the native structure of a protein is known and representing each intermediate conformation as a collection of fully folded structures in which each of them contains a set of interacting secondary structure elements, we show that it is possible to significantly reduce the conformation space while still being able to predict the most energetically favorable folding pathway of large proteins with hundreds of residues at the mesoscopic level, including the pig muscle phosphoglycerate kinase with 416 residues. The model is detailed enough to distinguish between different folding pathways of structurally very similar proteins, including the streptococcal protein G and the peptostreptococcal protein L. The model is also able to recognize the differences between the folding pathways of protein G and its two structurally similar variants NuG1 and NuG2, which are even harder to distinguish. We show that this strategy can produce accurate predictions on many other proteins with experimentally determined intermediate folding states. CONCLUSION: Our technique is efficient enough to predict folding pathways for both large and small proteins at the mesoscopic level. Such a strategy is often the only feasible choice for large proteins. A software program implementing this strategy (SSFold) is available at http://faculty.cs.tamu.edu/shsze/ssfold.

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. Publishing Authors By Initials

For similar abstracts research abstracts see: abstracts research

PUBMED ID PMID:

MEDLINE DATE:

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: BMC bioinformatics

VOLUME: 9

Page Numbers: 320

Journal Abbreviation: BMC Bioinformatics

ISSN: 1471-2105

DAY: 23

MONTH: 07

YEAR: 2008

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 100965194

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. Keywords Mesh Terms:

KEYWORDS:

MESH TERMS:

Chemical & Substance for Abstract: Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. Information

Substance Name:

Registry Number:

Grant and Affiliation Information for Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements.

AFFILIATION: Department of Computer Science, Texas A&M University, College Station, TX 77843, USA. qingwu-yang@neo.tamu.edu

Country: England

AGENCY:

GRANT:

ACRONYM:

MEDLINETA: BMC Bioinformatics

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements Related Publications

• 1.55-mum and infrared-band photoresponsivity of a Schottky barrier porous silicon photodetector.
• A distinct endosomal Ca2+/Mn2+ pump affects root growth through the secretory process.
• Advancing techniques in spinal MR imaging: but are they necessary for spinal leptomeningeal tumor?
• Benign lumbar arachnoiditis: MR imaging with gadopentetate dimeglumine.
• Benign lumbar arachnoiditis: MR imaging with gadopentetate dimeglumine.
• Catheter-directed embolectomy, fragmentation, and thrombolysis for the treatment of massive pulmonary embolism after failure of systemic thrombolysis.
• Concerning Need of Physicians for Posts in China.
• Cranial osteopetrosis: MR findings.
• Development of taxol and other endophyte produced anti-cancer agents.
• Diseases of the intracranial meninges: MR imaging features.
• Effects of dissolved oxygen, pH, and anions on the 2,3-dichlorophenol degradation by photocatalytic reaction with anodic TiO(2) nanotube films.
• Emergency retrieval of a G2 filter after complete migration into the right ventricle.
• Gravity force transduced by the MEC-4/MEC-10 DEG/ENaC channel modulates DAF-16/FoxO activity in Caenorhabditis elegans.
• Large-scale analysis of gene clustering in bacteria.
• Leptomeningeal tumor: the "plain vanilla" approach remains the best.
• MR imaging of the spinal cord: current status and future advances.
• MR of primary extraosseous Ewing sarcoma.
• Multiple sequence alignment based on profile alignment of intermediate sequences.
• Novel polymer composite to eliminate background matrix ions in matrix assisted laser desorption/ionization-mass spectrometry.
• Posterior interhemispheric transcallosal approach to pineal region tumors.
• Predicting neuropsychological development from skull imaging.
• Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements.
• Presence of Hoechst low side populations in multiple myeloma.
• Staphylococcal pneumonia and empyema in infancy.
• Symbolic shape descriptors for classifying craniosynostosis deformations from skull imaging.
• Targeting P-glycoprotein for Effective Oral Anti-Cancer Chemotherapeutics.
• The greater omentum.
• Today's Global Frontiers in Public Health: II. Regional Health Organization in the Far East.
• Totally cystic schwannoma of the tenth cranial nerve mimicking an epidermoid.
• Vasculitis presenting as primary leptomeningeal enhancement with minimal parenchymal findings.