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Scientists move toward rational design of artificial proteins

In the world of proteins, form defines function. Based on interactions between their constituent amino acids, proteins form specific conformations, folding and twisting into distinct, chemically directed shapes. The resulting structure dictates the proteins’ actions; thus accurate modeling of structure is vital to understanding functionality.

Peptoids, the synthetic cousins of proteins, follow similar design rules. Less vulnerable to chemical or metabolic breakdown than proteins, peptoids are promising for diagnostics, pharmaceuticals, and as a platform to build bioinspired nanomaterials, as scientists can build and manipulate peptoids with great precision. But to design peptoids for a specific function, scientists need to first untangle the complex relationship between a peptoid's composition and its function-defining folded structure.

Past efforts to predict protein structure have met with limited success, but now a scientific team led by Glenn Butterfoss, and Barney Yoo, research scientists at New York University, in collaboration with investigators from the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab), Stony Brook University, and Temple University have demonstrated that a computer modeling approach similar to one used to predict protein structures can accurately predict peptoid conformation as well.

The authors describe this accomplishment in a paper in the Proceedings of the National Academy of Sciences(PNAS) titled, "De novo structure prediction and experimental characterization of folded peptoid oligomers," coauthored by Jonathan Jaworski, Ilya Chorny, Ken Dill, Ronald Zuckermann, Richard Bonneau, Kent Kirshenbaum, and Vincent Voelz.

"Natural selection has engineered protein sequences that can self-assemble into molecular machines with specific functions. Why can't we do the same with biologically inspired synthetic materials?" Voelz, principal investigator with Temple University, explains.

With this mission in mind, the collaborative team of scientists developed the project two years ago (2010) at the 7th Peptoid Summit, a conference devoted to peptoid research hosted by Berkeley Lab’s Molecular Foundry.

"The research was carried out by a remarkable, interdisciplinary team of scientists," says Kent Kirshenbaum of NYU. "Some of the team have worked together on this truly difficult problem for almost 20 years. The researchers include both experimentalists and theorists who have been able to guide one another in discovering how these peptoid molecules fold."

Together, they proposed a 'blind structure prediction' challenge. This self-assessment technique, responsible for the enormous progress in the world of protein structure modeling, allows scientists to test the fidelity of their computational models by predicting the three-dimensional structure of a known molecule and then comparing their proposed structure to the X-ray crystallography results.

An analogous, combined experimental-computational method was employed by the peptoid team in an effort to advance the computational design of peptoid structure. X-ray crystal structures for three peptoid molecules, two small and linear and one larger and cyclical, were simultaneously determined, but not disclosed to the theoretical modelers. The experimentalists then used a combination of two simulation techniques, Replica Exchange Molecular Dynamics (REMD) simulation and Quantum Mechanical refinement (QM). REMD can efficiently predict the preferred general conformations, and the QM calculations further refine the conformational prediction. In combination, these two calculations accurately define the physical structures of molecules.

The proposed structural predictions of the peptoid molecules did exceedingly well at calculating the actual folded conformations. The first two blind predictions were calculated for two linear, small N-alkyl and N-aryl peptoid trimers. Of these, the N-aryl peptoid trimer was the best blind prediction, matching the crystal described conformation to within 0.2 Å. The N-alkyl trimer prediction matched less well with the crystal results because of its increased flexibility.

The greater challenge facing the group was structural prediction of the larger, cyclic peptoid nonamer. Six different possible conformations were considered for the final, submitted prediction and the top pick proved to agree best with the crystallography results to an accuracy of 1.0 Å.

This success suggests that reliable structure prediction for complex three-dimensional folds is within reach, an enormous step forward on the path to reliable and efficient computational peptoid design.

"This will hopefully break open the field of peptoid structure prediction and design, an area we desperately need to guide our more well-developed synthetic efforts," says Ron Zuckermann, co-author and director of the Biological Nanostructures Facility at Berkeley Lab's Molecular Foundry.

"It is an exciting time for peptoid research," says author Glenn Butterfoss, research scientist with NYU. "The community of labs working on these molecules is growing, and both the diversity and creativity of recent studies is quite astonishing. We hope our work here, aimed toward understanding the structural behavior of peptoids in three dimensional space, serves as a building block for future efforts to design peptoid molecules with practical functions."

Source: http://www.rdmag.com/News/2012/08/Life-Sciences-Scientists-Move-Toward-Rational-Design-Of-Artificial-Proteins/

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Founded by Russian entrepreneur Dmitry Itskov in February 2011 with the participation of leading Russian specialists in the field of neural interfaces, robotics, artificial organs and systems.

The main goals of the 2045 Initiative: the creation and realization of a new strategy for the development of humanity which meets global civilization challenges; the creation of optimale conditions promoting the spiritual enlightenment of humanity; and the realization of a new futuristic reality based on 5 principles: high spirituality, high culture, high ethics, high science and high technologies. 

The main science mega-project of the 2045 Initiative aims to create technologies enabling the transfer of a individual’s personality to a more advanced non-biological carrier, and extending life, including to the point of immortality. We devote particular attention to enabling the fullest possible dialogue between the world’s major spiritual traditions, science and society.

A large-scale transformation of humanity, comparable to some of the major spiritual and sci-tech revolutions in history, will require a new strategy. We believe this to be necessary to overcome existing crises, which threaten our planetary habitat and the continued existence of humanity as a species. With the 2045 Initiative, we hope to realize a new strategy for humanity's development, and in so doing, create a more productive, fulfilling, and satisfying future.

The "2045" team is working towards creating an international research center where leading scientists will be engaged in research and development in the fields of anthropomorphic robotics, living systems modeling and brain and consciousness modeling with the goal of transferring one’s individual consciousness to an artificial carrier and achieving cybernetic immortality.

An annual congress "The Global Future 2045" is organized by the Initiative to give platform for discussing mankind's evolutionary strategy based on technologies of cybernetic immortality as well as the possible impact of such technologies on global society, politics and economies of the future.


Future prospects of "2045" Initiative for society


The emergence and widespread use of affordable android "avatars" controlled by a "brain-computer" interface. Coupled with related technologies “avatars’ will give people a number of new features: ability to work in dangerous environments, perform rescue operations, travel in extreme situations etc.
Avatar components will be used in medicine for the rehabilitation of fully or partially disabled patients giving them prosthetic limbs or recover lost senses.


Creation of an autonomous life-support system for the human brain linked to a robot, ‘avatar’, will save people whose body is completely worn out or irreversibly damaged. Any patient with an intact brain will be able to return to a fully functioning  bodily life. Such technologies will  greatly enlarge  the possibility of hybrid bio-electronic devices, thus creating a new IT revolution and will make  all  kinds of superimpositions of electronic and biological systems possible.


Creation of a computer model of the brain and human consciousness  with the subsequent development of means to transfer individual consciousness  onto an artificial carrier. This development will profoundly change the world, it will not only give everyone the possibility of  cybernetic immortality but will also create a friendly artificial intelligence,  expand human capabilities  and provide opportunities for ordinary people to restore or modify their own brain multiple times.  The final result  at this stage can be a real revolution in the understanding of human nature that will completely change the human and technical prospects for humanity.


This is the time when substance-independent minds will receive new bodies with capacities far exceeding those of ordinary humans. A new era for humanity will arrive!  Changes will occur in all spheres of human activity – energy generation, transportation, politics, medicine, psychology, sciences, and so on.

Today it is hard to imagine a future when bodies consisting of nanorobots  will become affordable  and capable of taking any form. It is also hard to imagine body holograms featuring controlled matter. One thing is clear however:  humanity, for the first time in its history, will make a fully managed evolutionary transition and eventually become a new species. Moreover,  prerequisites for a large-scale  expansion into outer space will be created as well.


Key elements of the project in the future

• International social movement
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