Much of what is known about protein dynamics has been studied using bulk biochemical techniques and chemical denaturants. By contrast, we study proteins at the single molecule level and use mechanical forces to denature proteins. Force is a ubiquitous denaturant in biology. Our results are opening new vistas into protein function and challenging some widely accepted views of protein dynamics.
Courses taught at Columbia University:
- Frontiers of Science, Science C1000
- The Biology and Physics of Single Molecules, Biology Biology W4070
- Cellular Physiology of Disease, Biology W3008/W4008
- Student evaluations: Dr. Fernandez is the BEST professor I have had a Columbia, hands down. I wish I had met him my first year here; Best Biology professor that I've ever encountered at Columbia. Very rare find! He is very clear and available for questions, and I've enjoyed going to office hours; Really wonderful teacher who genuinely wants his students to be as fascinated with the material as he is.
Research stats:148 publications,~13000 citations, h~60
Ambition: revolutionize protein biochemistry through the use of single molecule force-spectrsocopy.
In 2008, after 4 years in Dr. Michael NILGES group at the Institut Pasteur of Paris; I graduated in Molecular Biophysics from the Université Denis Diderot of Paris VII. My research concerned the discovery of new drugs against different therapeutic targets of Plasmodium falciparum and Mycobacterium tuberculosis. I used different computer aided techniques such as homology modeling and high throughput docking to identify and develop inhibitors.
Afterwards, I joined the lab of Prof. Pedro ALZARI to learn crystallography. My research focused on characterizing hit compounds identified during my PhD training and studying the mechanism of an essential mycobacterial glycosyltransferase. Based on new Xray structures, this work outlines the fundamental role of conformational changes induced by the binding to the membrane and its different substrates. This experience also tackled the actual limits of structure-based drug design on flexible enzymes.
I am currently working on elastic properties of titin, the gigantic protein connecting actin and myosin in the sarcomere.
I obtained my B.Sc. degree in Chemical Engineering from Gh. Asachi Technical University (Iasi, Romania), as head of his class (out of 250 students). I did my Ph.D. at University of Geneva (Switzerland), in the area of Physical and Analytical Chemistry, with focus on colloids, polymers and surface chemistry. There I conducted research under the supervision of prof. Michal Borkovec using the Atomic Force Microscope (AFM) to measure interaction forces in colloidal probe and single molecule force spectroscopy modes and to prepare and characterize nano-patterned surfaces. The main subject of my Ph.D. was to measure and understand the interactions appearing between heterogeneously charged surfaces using force applying techniques, such as AFM . During my Ph.D. I was awarded for my research with the SCS-Mettler-Toledo-Prize, given by the Swiss Chemical Society at the SCS Fallmeeting (Zürich, Switzerland, 2008) and I was selected to participate to the 59th Lindau Nobel Laureates Meeting, between Nobel Laureates and International Best Talents (Lindau, Germany, 2009). For my post-graduate research training I moved to Columbia University, in the lab of prof. Julio M. Fernandez, in the Biological Sciences Department. In my first year in Fernandez lab I have studied thermal effects on the mechanical unforlding of polyproteins. For this I have developed a setup capable of conducting force-clamp spectroscopy under controlled temperature conditions. I am currently involved in a research project aiming at determining the molecular mechanisms that control protein extensibility using a combination of magnetic tweezers and Total Internal Reflection Fluorescence (TIRF).
I obtained my PhD in 2012 from University of Chile (Santiago, Chile) under the supervision of Dr. Victoria Guixe, at the Biological Sciences Department. My work there was related to understanding the conformational changes that thermophilic proteins undergo in solution. We used different techniques to determine the kinetic mechanisms and biophysical properties of glycolytic enzymes from hyperthermophilic organisms.
I joined the lab in September 2012, with the intent of studying protein conformational transition but this time at single molecule level. I currently use the enzyme glucokinase as a model to study the transition triggered by ligand from the Open to the Closed conformation. Also, I am involved in several projects with different members of Professor Fernandez's lab, trying to understand the function of posttranslational modifications on folding pathways of mechanical proteins.
I obtained my PhD from Complutense University (Madrid, Spain) in 2008. I developed my research under the supervision of Drs. Á. Martínez del Pozo and J. G. Gavilanes, at the Department of Biochemistry and Molecular Biology I. I studied the mechanism of pore formation by a family of eukaryotic pore-forming toxins, the actinoporins from sea anemones. We employed a variety of biochemical and biophysical approaches to understand how actinoporins interact with lipid membranes and the subsequent conformational changes they experience.
In May 2008 I joined Julio Fernandez lab. Since then, I have been subdued by the new possibilities single-molecule techniques offer to biologists. I have been involved in projects dealing with protein mechanics, such as the realization that intramolecular isopeptide bonds in adhesins of gram-positive bacteria confer unprecedented mechanical stability to protein domains. We have also implemented an assay based on mechanical uncaging of cysteine residues that allowed us to monitor in real-time the isomerization of disulfide bonds in proteins. My current research projects try to bridge the gap between Protein Mechanics and Biology. I want to know how the mechanical properties of proteins determine the macroscopic behavior of tissues and cells. Pili from Gram-positive bacteria are natural polyproteins that have to overcome high mechanical stress in vivo. Using force-spectroscopy, we can dissect the mechanical properties of pili components. We are trying to understand how mechanically defective pili are challenged when adhering under mechanical stress. Our strategy may be useful to design new antibiotics that interfere with the attachment of pathogenic bacteria.
Pallav Kosuri graduated this summer with a PhD in Biochemistry and Molecular Biophysics from Columbia University. Prior to Columbia, he completed his Bachelors and Masters degrees in Physics from the Royal Institute of Technology in Stockholm, Sweden, and did his thesis research at the European Center for Nuclear Research (CERN) in Geneva, Switzerland. After a brief stint as a photojournalist, he was awarded a Fulbright scholarship and joined the Fernandez Lab, where he studies how enzymes are involved in protein synthesis and folding. Using force spectroscopy, he has developed new methods to track the formation of individual chemical bonds in single protein molecules. Pallav also works on the development of a new Atomic Force Microscope, and together with Raul Perez-Jimenez explores the emerging interdisciplinary field of Paleoenzymology.
Some of Pallav's photographs can be seen here:
I obtained my Ph.D. degree in Physical Chemistry from the University of Granada under the supervision of Dr. Jose M. Sanchez-Ruiz and Dr. Beatriz Ibarra-Molero. My thesis work focused mainly in an attempt to define the role of surface charge interactions in protein stability as well as the study of the evolutive information obtained from sequence alignments and its consequences in protein folding, structure and stability. My interest now is focused in the study of the protein folding as well as the mechanical stability using Single Molecule Force Spectroscopy. The techniques developed in Dr. Fernandez's Lab have become a powerful tool for the study of protein folding/unfolding processes under a stretching force in a new manner that reveals features of proteins non accessible with bulk techniques. I am interested in the use of the Force-clamp techniques to understand how a protein finds the way to fold into a native state and what are the more important aspects involved.
In 2002 I have graduated (BSc) the Technion (Israeli Institute of Technology) in Chemical Engineering. During my undergrad studies I have worked with Prof. Yaron Paz and Dr. Ori Ramon on a project of understanding coil to globule transition in hydrophobic polymers. After my graduation I have worked as an engineer in IMI LTD, there I worked in the engineering department, and also became a manufacturing department manager (crystallization and coating processes). In 2006 I started my PhD (direct) in theoretical chemical-physics under the supervision of Prof. Yossi Klafter and Prof. Michael Urbakh, in the exact science dept. in Tel-Aviv University. My PhD thesis focuses on modeling diffusion in biophysical systems using the statistics of stochastic processes, developing algorithms for both calculations and simulations of those processes, optimizing and analyzing parameters of multi-particles systems using Monte-Carlo algorithms. In my main projects I have applied the Jarzynski equation to frictional systems, modeled single molecule collapse of force induced extended protein and build analytical FRAP model (backed up with simulations and experiments). I have joined Prof. Julio Fernandez group in April 2010, in order to expand my knowledge on the way that mechanical force affects biophysical systems in a single molecule level and to learn and profess in experimental methods.
I am a second year PhD student in the Biochemistry and Molecular Biophysics program at Columbia. I received my undergraduate degree in 2011 from the University of Southern California, where I worked in the lab of Dr. Mohamed El-Naggar. My research there focused on microbial fuel cells and bacterial extracellular electron transfer. I joined the Fernandez lab in January 2012. My research interests primarily consist of the effects of mutations or oxidative cysteine adducts on the mechanical stability and refolding kinetics of titin, a large elastic protein found in all types of muscle. Through a collaboration with Dr. Lawrence Shapiro in the Biochemistry department at Columbia, I’ve been working to obtain crystal structures of various modified titin domains. My aim is to provide a quantitative structural basis to accompany the results of the force spectroscopy experiments obtained by my colleagues. My goals are to advance the understanding of the interplay between structure and mechanical stability, and to shed light on the molecular mechanisms of cardiomyopathy, infarction, and other heart disorders.
Ethan is a third-year undergraduate student at Columbia University in New York City, and is currently working toward degrees in Biochemistry and Philosophy. Ethan joined the Fernandez lab in 2012 as a Summer Undergraduate Research Fellow after spending two years in the laboratory of Dalibor Sames (Department of Chemistry) where his research focused on diverse topics in neurochemistry. As a member of the Fernandez lab, and in collaboration with Dr. Raul Perez-Jimenez, Ethan's research has focused on the application and development of the method of Paleoenzymology (see Research tab above). Ethan is working on improving the computational aspects of this method, as well as preparing and performing molecular biological experiments on the predicted proteins.
Outside of the lab, Ethan is an award-winning classical guitarist, and has worked as a Department Head at the Columbia University Radio Station (WKCR), as well as an opinion columnist for the Columbia Spectator. When not performing empirical research, Ethan works toward introducing a cogent philosophy of science in the lab, while using his knowledge of topics in this area to inform new directions for his own research. Ultimately, Ethan aims to renew the significance of philosophy for scientific researchers by reinvigorating the role philosophers can play in the laboratory setting.
Jason Feng is an undergraduate student at Columbia College and a summer undergraduate research fellow currently pursuing a B.A. in mathematics/philosophy.
Jason is working on detecting the pKa of small molecules as they interact with protein substrates on a single molecule level via atomic force microscopy.
In his spare time, Jason enjoys table tennis, bonsai, and considering the meaning of existence.
Kevin is a undergraduate in the Class of 2015 at Columbia College pursuing a degree in biochemistry. In the lab, Kevin is now working on a comprehensive structural analysis of titin's immunoglobulin domains and the regulation of the titin elasticity.
After graduation, Kevin hopes to continue his education in medical school pursuing his desire to work in the medical field.
In his free time, he enjoys following his favorite sports teams from his home state of Texas, including the Cowboys, Rangers, and Mavericks.
Molecular Biologist and lab manager
I am in charge of the molecular biology section of the laboratory. I engineer most of the polyproteins that we use. We have a well established protocol for constructing polyproteins at the DNA level and then expressing them in bacteria. I use Talon columns and FPLC for protein purification. We struggle a bit with engineering AFM ready polyproteins. Not all of them give nice pulls. If so, I am the one that usually gets to re-engineer and/or re-express the proteins. I teach all the lab members how to do it and also I am happy to help other investigators by phone and email. I welcome inquiries.
I keep the lab running smoothly. I work together with Carmelu in the molecular engineering and synthesis of the proteins we use. I am helping out with a variety of scientific projects included but not limited to studies in Corynebacterium diphtheria.
Outside the lab I enjoy outdoors activities, specially rock climbing and birdwatching.
Former postdoctoral students in tenured/tenure-track academic positions:
Raul Perez-Jimenez, Ph.D.; Nanogune, San Sebastian, Spain
Sergi Garcia-Manyes, Ph.D.; Physics, Kings College London, U.K.
Jasna Brujic, Ph.D.; Physics, New York University, U.S.
Frauke Graeter, Ph.D.; Heidelberg Institute for Theoretical Studies, Germany
Sri Rama Koti Ainavarapu, Ph.D.; Chemical Sciences, Tata Institute of Fundamental Research, India
Ruchuan Liu, Ph.D.; Physics, NUS, Singapore
Robert Szoszkiewicz, Ph.D.; Physics, Kansas State University, U.S.
Hongbin Li, Ph.D.; Chemistry, University of British Columbia, Canada
Mariano Carrion Vazquez, Ph.D.; Cajal Institute, Madrid, Spain
Thomas Fisher, Ph.D.; Physiology, University of Saskatchewan, Canada
Piotr Marszalek, Ph.D.; Engineering, Duke University, U.S.
Andres Oberhauser, Ph.D.; Biochemistry & Molecular Biology, UTMB, U.S.
Brenda Farrell, Ph.D.; Department of Otolaryngology, Baylor College of Medicine, U.S.
Vladimir Parpura, MD/Ph.D.; Neurobiology, University of Alabama at Birmingham, U.S.
Keiju Okano, Ph.D.; Cell Biology, Akita Prefectural University, Japan
Iain Robinson, Ph.D.; Neurobiology, The Peninsula College of Medicine and Dentistry, U.K.
Guillermo Alvarez de Toledo, Ph.D.; Physiology & Biophysics, University of Seville, Spain
Former graduate students doing postdoctoral work:
Arun Wiita, MD/Ph.D.; Pharmaceutical Chemistry, UCSF, U.S.
Rodolfo Hermans, Ph.D.; London Center for Nanotechnology, U.K.
Kirstin Walther, Ph.D.; Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
Former technicians studying towards a Ph.D. degree:
Hector Huang; Dept. Chemistry, University of California, Berkeley, CA
Judith Latimer; Chemistry and Chemical Engineering, Caltech, CA
Shayna Busch; Math-Biology, University of Miami, FL
Wolfgang Linke, Ph.D.; Cardiovascular Physiology, Ruhr University Bochum, Germany
Carles Solsona, Ph.D.; Cell Biology, Universitat de Barcelona, Spain
Vladislav Markin, Ph.D.; Neurology and Neurotherapeutics, UT Southwestern, U.S.