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 carried out my MSci degree in Physics and Astronomy at the University College London. Once I graduated I moved to Grenoble (France) to do a Ph.D in applied soft matter physics given by the École Normale Supérieure (ENS) de Lyon. The research project was co-supervised by Prof. Michel Peyrard from the ENS, and Dr. Andrew Wildes from the Institute Laue-Langevin, a world leading neutron facility, where I performed most of my research. During my Ph.D I investigated the structural and dynamical properties of fibre samples made of oriented DNA molecules. The high orientation of these samples allowed us to study the dynamical fluctuations and the melting transition of DNA using neutron and X-ray scattering. Furthermore, I implemented these studies with a variety of experimental techniques such as differential scanning calorimetry in collaboration with Jean-Luc Garden and Jacques Richard from CNRS, Grenoble.
I am very interested in studying the mechanical and dynamical properties of biological phenomena, such as protein folding, from a single-molecule approach. That is why I recently become part of Fernandez’s lab as a postdoctoral researcher. My role in the lab is to lead the development of an unified physical model of the energy landscape of titin combining the genetic information and its elastic properties. The ultimate goal will be to use the model to predict the severity of diseases resulting from abnormal cellular regulation and from genetic mutations in the titin gene.
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.
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.
I am a second year student in the MD/PhD program at Columbia. I graduated from Princeton University with an A.B. in Chemistry, though with perhaps an equal amount of class time invested in Kiswahili literature and global health. I did my undergraduate thesis research in the lab of Dr. Michael Hecht, where I studied the biological potentials of de novo-designed proteins, and thereafter went to work with Dr. J. Dirk Iglehart and Dr. J.B. Lazaro in cancer biology at the Dana Farber Cancer Institute. Since joining the Fernandez lab in Summer 2013, my research interests have focused on the determinants of mechanical stability in proteins, and on the mechanisms of bacterial adherence under force, with an eye towards developing new strategies for preventing bacterial colonization.
I am a third year MD/PhD student at Columbia University. I received my undergraduate degrees in chemical engineering and chemistry from the University of Pennsylvania in 2011. While at Penn, I worked in the lab of Dr. Dennis Discher studying the effects of tissue elasticity on gene expression and stem cell differentiation. After completing two years of clinical coursework and several clinical rotations, I joined the Fernandez lab for my thesis research. I am interested in the mechanical modulation of elastic protein titin and its implications in dilated cardiomyopathy. I hope to apply techniques of single molecule force measurement to understand differential signalling of proteins in their folded and unfolded states.
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.
Jaykar is a second year undergraduate student at Columbia College majoring in Applied Mathematics. He previously worked in the laboratory of Dr. Carolyn Bondy in the NIH where his research focused on epigenetic aspects of turner syndrome. Jaykar is now working on creating a computer simulation of Titin.
After graduation, Jaykar would like to work for a start-up. In his free time he enjoys watching T.V., and playing chess.
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 graduated from Columbia University with a B.A. in Biophysics in 2013. I spent two years working in the lab of Lars Dietrich in the Biological Sciences department. My research concerned several aspects of the biofilm development of the Gram-negative pathogenic bacterium Pseudomonas aeruginosa PA14, including the chemical signaling that drives biofilm morphogenesis and the importance of the production of extracellular matrix for biofilm survival.
I joined the Fernandez lab in May 2013. I work with Carmelu in the molecular biology section of the laboratory to clone, express, and purify the polyproteins used for single molecule force spectroscopy experiments. I also handle many of the day-to-day operations required to keep the lab running smoothly.
Former postdoctoral students in tenured/tenure-track academic positions:
Ronen Berkovich, Ph.D.; Chemical Engineering, Ben-Gurion University, Israel
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:
Pallav Kosuri, PhD.; Department of Chemistry & Chemical Biology, Harvard University
Arun Wiita, MD/Ph.D.; Pharmaceutical Chemistry, UCSF.
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:
Diego Rojas; Teachers College, Columbia University, NY
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.