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Intrinsic Changes In Protein Shape Influence Drug Binding
ScienceDaily (Aug. 24, 2009) — Computational biologists at the University of Pittsburgh School of Medicine have shown that proteins have an intrinsic ability to change shape, and this is required for their biological activity. This shape-changing also allows the small molecules that are attracted to a given protein to select the structure that permits the best binding. That premise could help in drug discovery and in designing compounds that will have the most impact on protein function to better treat a host of diseases.
See also:
Health & Medicine
* HIV and AIDS
* Pharmacology
* Human Biology
Plants & Animals
* Biotechnology
* Genetics
* Molecular Biology
Reference
* Drug discovery
* Protein microarray
* Antiviral drug
* Protein folding
The findings were published this week in the online version of the Proceedings of the National Academy of Sciences.
According to the classical view, known as "induced fit," drug binding causes a change in the target protein structure, explained senior author Ivet Bahar, Ph.D., professor and John K. Vries Chair of the Department of Computational Biology, Pitt School of Medicine. But it now appears that a protein has many different conformations that are already available even without the presence of a binding molecule, which is called the ligand. The ligand attaches to the protein shape that allows it to fit well, and that close interaction can lead to effective inhibition of protein function.
Gathering information about the array of conformations a target protein might exhibit can be of great use when designing new drugs, Dr. Bahar said. That allows the scientist to better identify the structural pocket into which the drug must fit to cause significant alterations in protein function, such as the inhibition of an enzyme reaction.
For the study, Dr. Bahar and her doctoral student, Ahmet Bakan, focused on three common drug targets, namely enzymes important in HIV, inflammatory response and the cell division cycle. Using the sets of conformations of protein-ligand complexes stored in the Protein Data Bank, an information repository for the scientific community at Rutgers University, the researchers figured out what structures the enzymes had both alone and when bound to a variety of small molecules.
"It seems there are simple but robust rules that control ligand binding," Dr. Bahar explained. "If we know the rules, we can make better predictions about which binding sites to target to make more effective drugs."
Dr. Bahar's research is funded by the National Institutes of Health.
Adapted from materials provided by University of Pittsburgh Schools of the Health Sciences, via EurekAlert!, a service of AAAS.
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Proteins' Internal Motion Found To Affect Their Function: Implications For Drug Design (July 20, 2007) — Penn investigators are the first to observe and measure the internal motion inside proteins, revealing how this affects their function. This overturns the standard view of protein structure-function ... > read more
Breaking Down Huntington's Disease One Protein At A Time (Feb. 8, 2008) — Hoping to piece together the intricate series of interactions that lead to Huntington's disease, scientists have determined the shape and structure of a binding site that may prove useful in ... > read more
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Science News
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Intrinsic Changes In Protein Shape Influence Drug Binding
ScienceDaily (Aug. 24, 2009) — Computational biologists at the University of Pittsburgh School of Medicine have shown that proteins have an intrinsic ability to change shape, and this is required for their biological activity. This shape-changing also allows the small molecules that are attracted to a given protein to select the structure that permits the best binding. That premise could help in drug discovery and in designing compounds that will have the most impact on protein function to better treat a host of diseases.
See also:
Health & Medicine
* HIV and AIDS
* Pharmacology
* Human Biology
Plants & Animals
* Biotechnology
* Genetics
* Molecular Biology
Reference
* Drug discovery
* Protein microarray
* Antiviral drug
* Protein folding
The findings were published this week in the online version of the Proceedings of the National Academy of Sciences.
According to the classical view, known as "induced fit," drug binding causes a change in the target protein structure, explained senior author Ivet Bahar, Ph.D., professor and John K. Vries Chair of the Department of Computational Biology, Pitt School of Medicine. But it now appears that a protein has many different conformations that are already available even without the presence of a binding molecule, which is called the ligand. The ligand attaches to the protein shape that allows it to fit well, and that close interaction can lead to effective inhibition of protein function.
Gathering information about the array of conformations a target protein might exhibit can be of great use when designing new drugs, Dr. Bahar said. That allows the scientist to better identify the structural pocket into which the drug must fit to cause significant alterations in protein function, such as the inhibition of an enzyme reaction.
For the study, Dr. Bahar and her doctoral student, Ahmet Bakan, focused on three common drug targets, namely enzymes important in HIV, inflammatory response and the cell division cycle. Using the sets of conformations of protein-ligand complexes stored in the Protein Data Bank, an information repository for the scientific community at Rutgers University, the researchers figured out what structures the enzymes had both alone and when bound to a variety of small molecules.
"It seems there are simple but robust rules that control ligand binding," Dr. Bahar explained. "If we know the rules, we can make better predictions about which binding sites to target to make more effective drugs."
Dr. Bahar's research is funded by the National Institutes of Health.
Adapted from materials provided by University of Pittsburgh Schools of the Health Sciences, via EurekAlert!, a service of AAAS.
Email or share this story:
| More
Need to cite this story in your essay, paper, or report? Use one of the following formats:
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Related Stories
Proteins' Internal Motion Found To Affect Their Function: Implications For Drug Design (July 20, 2007) — Penn investigators are the first to observe and measure the internal motion inside proteins, revealing how this affects their function. This overturns the standard view of protein structure-function ... > read more
Breaking Down Huntington's Disease One Protein At A Time (Feb. 8, 2008) — Hoping to piece together the intricate series of interactions that lead to Huntington's disease, scientists have determined the shape and structure of a binding site that may prove useful in ... > read more
Dance By Protein Linked To Parkinson's And Alzheimer's Diseases Reveals Unprecedented Twists And Turns (Mar. 24, 2009) — Much remains to be understood about what role alpha-synuclein, a protein mostly associated with Parkinson's disease, plays in the brain, either in a normal or diseased state. Researchers have now ... > read more
Most Stable Parts Of Protein Are The First To Fold, Study Finds (Sep. 15, 2006) — Like a 1950's Detroit automaker, it appears that nature prefers to build its proteins around a solid, sturdy chassis. A new study combining advanced computational modeling and cutting-edge ... > read more
Search ScienceDaily
Number of stories in archives: 44,032
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Just In:
Lightning's Mirror Image ... Only Much Bigger
Using Light To Teach Magnets New Tricks
Microchip Does 1,000 Chemical Reactions At Once
Naming Evolution's Winners And Losers
Inner 'Fingerprint' For Personal Medical Care
Why Sleep? To Boost Efficiency, Minimize Risk
Ultrathin LEDs: New Class Of Displays
Oxycholesterol: Greatest Heart Disease Risk?
Science Video News
Low-Fat Fried Food?
Deep-fried fish could get healthier with a new protein-based batter extracted from the muscle of discarded fish parts. When coated onto the fish it. ... > full story
* Optical Scientists, Psychiatrists Develop Minimally Invasive Eye Test for Alzheimer's
* Biochemists Develop Proteomic Test For Breast Cancer
* Neuroendocrinologists Unlock Chemical Trigger to Puberty
* more science videos
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* S.Korea seeks 4-year prison term for stem cell fraud
* Encyclopedia of Life grows; clues on ageing, pests
* Satellites put into orbit for Japan and Australia
* Scientists make "sugar bug" drug for bowel disease
* Gene swap experiment makes altering bugs easier
* more science news
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* Justice Dept advises pursuing CIA abuses: report
* Suspect in U.S. model murder found dead in Canada
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* U.S. presses sanctions to end N.Korea atomic plans
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