RANGANATHAN LAB
BMB | IME | Center for Physics of Evolving Systems
The University of Chicago
The Evolutionary Design of Biological Systems
From atomic to ecosystem scales, living systems exhibit exquisite structural and functional properties while yet remaining adaptive to fluctuating environmental conditions. We seek to find answers to three fundamental questions: what is the basic architecture of these systems, how do they work, and why are they built the way they are?
The Evolutionary Design of Biological Systems
From atomic to ecosystem scales, living systems exhibit exquisite structural and functional properties while yet remaining adaptive to fluctuating environmental conditions. We seek to find answers to three fundamental questions: what is the basic design of these systems, how do they work, and why are they built the way they are?
Research
We use a combination of statistical genomics, biochemistry, genetics in several model organsisms, structural biology, and physical theory to undestand the evolutionary design of proteins and macromolecular complexes.
People
Lab members come from vastly diverse backgrounds, and develop independent research programs within the core theme of the lab. Collaborations often emerge and open up new unexpected lines of thought.
Papers
Our publications. Concepts in our work are often developed over several papers, Thus, we provide summaries and notes that explain the contribution of each paper in context of overall laboratory themes.
Education
The didatic program within our lab comprises lectures, videos, and short notes that are developed and presented by the PI and all lab members.
Resources
We support open distribution of materials and knowledge developed in our laboratory. Download software tools, datasets, protein structures, and protocols.
News and Info…
new paper out…
Victor Salinas’ paper on “Coevolution-based inference of amino acid interactions underlying protein function” is out. Check it out here.
Two new students join the lab!
Craig DeValk, a first-year BMB graduate student has now started in the group, and is focusing on the use of forward evolution systems to understand how fluctuations in conditions of selection control (or not) the design of proteins. Also, Sarah Wasinger, a first-year undergraduate student with deep interests in molecular engineering will start in the lab next month.
Rama podcast…
As part of a new podcast series at the University of Chicago, Rama did an episode on evolution and design. Check it out here:
Relocation…
As of November 15, 2017 the Ranganathan Lab has moved to the University of Chicago. We are part of a new Center for Physics of Evolution, with departmental affiliations in Biochemistry & Molecular Biology and the Institute for Molecular Engineering.
The coolest new thing....
[Salinas et al., eLife 2018;7:e34300]. Protein function arises from still unclear pattern of cooperative interactions between amino acids. To address this, Victor Salinas in the lab has conducted a very large-scale analysis of pairwise thermodynamic mutant cycle couplings around the functional site of several homologs of a protein family. The work shows that protein function (here, ligand binding) arises from a sparse, cooperative, and evolutionarily conserved network of amino acids. Using these data as a benchmark for statistical coevolution methods, he shows that with different methods (SCA and DCA), coevolution reports both direct structural contacts and the cooperative mode that underlies function. We propose a simple thermodynamic model in which this functional mode represents a cooperative, two-state internal conformational equilibrium mediating function and allostery within the protein. Read about this work here…
Center for Physics of Evolution
Biochemistry & Molecular Biology
The Institute for Molecular Engineering
The University of Chicago
929 E. 57th Street
Chicago, IL 60637
