The research in Jose Onuchic's group is threefold. They theoretically study protein folding and function, molecular motors and electron transfer. Following are the key questions being inquired in the study of molecular motors.How is the chemical energy converted into mechanical work? How is the directionality of molecular movement determined? How is the molecular movement coordinated or regulated? Using structure-based simplified modeling, we try to understand the working principle of molecular motors. Our major goal has been to explore how these issues control the effective coupling in biopolymers. For this purpose, we have developed a framework, which included analytical methods and software tools.

http://guara.ucsd.edu/

 

Cells sense their environment, process information, and continuously react to both internal and external stimuli. The construction of synthetic gene networks can help improve our understanding of such naturally existing regulatory functions within cells. We use computer engineering principles of abstraction, composition, and interface specifications to program cells with sensors and actuators precisely controlled by analog and digital logic circuitry. Here, recombinant DNA-binding proteins represent signals, and recombinant genes perform the computation by regulating protein expression. We constructed synthetic gene networks that implement biochemical logic circuits using the AND, NOT, and IMPLIES logic gates. We have built a variety of circuits, behaving like digital and analog circuits. The integration of digital and analog circuitry is useful for controlling the behavior of individual cells and we have also combined these circuits with engineered cell-cell communication to coordinate the behavior of cell aggregates.

http://weisswebserver.ee.princeton.edu/index.php

 

Direct elucidation of the mechanisms governing molecular self-assembly has clear implications for understanding and possibly controlling processes ranging from the crystallization of biomolecules and pharmaceutics to the formation of protein complexes and the interaction of protein and drug molecules with cellular membranes and biomimetic substrates. The ability to acquire in situ real-space information would thus represent a significant advance towards understanding the kinetics and mechanics of molecular self-assembly. Our research program focuses on the application of in situ scanning probe microscopy in combination with other biophysical characterization techniques including circular dichroism, light scattering, X-ray scattering, NMR spectroscopy, and infrared and Raman spectroscopy to the study of self-assembled systems ranging from molecular and protein crystallization to the formation of ligand complexes and direct measurement of intermolecular forces.

http://linus.ibme.utoronto.ca/YipLab/index.html

 

Force is a ubiquitous modulator of protein function in biology. We have developed single molecule AFM techniques to study how mechanical forces affect the dynamics and chemistry of proteins. When polyproteins are extended by an AFM, their force properties are unique mechanical fingerprints that unambiguously distinguish them from the more frequent non-specific events that plague single molecule studies. We combine polyprotein engineering together with active force-clamp AFM techniques. With this approach, the length of an extending polyprotein is measured while the pulling force is actively kept constant by negative feedback control. We study the force dependency of protein folding, unfolding and chemical reactions. From the force dependence, we extract features of the transition state of these reactions that reveal underlying molecular mechanisms.

http://fernandezlab.biology.columbia.edu/

 

Research in the Ramamoorthy lab is focussed on membrane-associated biological systems, such as membrane proteins and antimicrobial peptides. We explore biological membranes in two different ways: Foremost, we develop and apply sophisticated solid-state NMR spectroscopy to study the structural properties of such systems. In parallel, we apply the whole array of standard biophysical methods to understand the energetics and dynamics of membrane-located biomolecules.

http://sitemaker.umich.edu/ramslab/home

 

We are investigating and developing a range of compounds that interact with different sequences and structures of DNA. We are particularly interested in the design drugs that can inhibit specific organisms by forming complexes in the DNA minor groove at unique sequences and structures of DNA or RNA. A range of solution and molecular modeling experiments are being conducted on minor groove complexes of compounds that interact with DNA oligomer sequences that mimic selected sequences from the organism to be targeted. These studies lead to a molecular model of the complex as a computer model, and logical variations of the drug structure to enhance the DNA interactions can be proposed and initially tested in the computer. We are particularly interested in developing new classes of agents that can interact with DNA as cooperative dimers. Such compounds have the ability to simultaneously recognize both strands of DNA to significantly enhance interaction strength and specificity. We are establishing rules for the specific interaction of heterocyclic dimers with DNA and we now have new types of compounds that can recognize a number of DNA sequences with high specificity.

http://chemistry.gsu.edu/Wilson.php

 

There are two things that motivate our research into stem cells: our desire to contribute to the health and welfare of Canadians and people all over the world; and, our interest in complex problems that can be explored through bioengineering. Research in my lab is focused on the generation of functional tissue from adult and embryonic stem cells. Our quantitative, technology-driven approach strives to gain new insight into the fundamental mechanisms that control the fate of stem cells, and to develop robust systems for the controlled generation of clinically relevant numbers of functional stem cells and their derivatives. We are specifically focused on the growth of human blood stem cells and the generation of blood and cardiac cells from embryonic stem cells. The long-term goal would be to generate transplantable blood stem cell and repair damaged tissues such as hearts with stem or progenitor cells.

http://tdccbr.med.utoronto.ca/members/peter_zandstra.html