Day 2 :
Keynote Forum
Joachim Krebs
MPI for Biophysical Chemistry Göttingen, Germany
Keynote: Regulation of the Calcium Pump of Plasma Membranes by Calmodulin
Time : 09:55-10:35
Biography:
Abstract:
Calcium is the third most abundant metal in nature and a versatile carrier of many signals within and outside the cell. Due to its peculiar coordination chemistry calcium is highly flexible as a ligand which enables it to regulate many important aspects of cellular activity. Calcium can fulfill its many different functions insite and out of the cell due to an integrated network of calcium channels, exchangers and pumps. In this presentation I will give an overview on our studies of the interaction and regulation of the plasma membrane calcium pump (PMCA) by calmodulin, and the importance of the spliced isoforms of PMCA with special emphasis on the possible regulation of expression of PMCA1a, the neuronal specific isoform of PMCA, by the thyroid hormone T3.
- Structural Biology | Sequence Analysis | Molecular Modelling
Location: Spreewald
Chair
Igor Sokolov
, Tufts University, USA
Session Introduction
Igor Sokolov
Tufts University, USA
Title: Quantitative and repeatable measurements of elastic moduli of cells
Biography:
Igor Sokolov is an expert in atomic force microscopy in studying cells and biological tissues. Being initially trained as a Physicist, he received Postdoctoral training
in Microbiology. He is the recipient of the E L Ginzton International Fellowship Award from Stanford University for his work on atomic force microscopy, he received
Graham Research Award (Clarkson University), Simon Greenberg Foundation Scholarship for the study of aging skin, etc., in 2000 he joined Clarkson University,
where he achieved the title of Full Professor and served as Director of the Nano-engineering and Biotechnology Laboratories Center. He has 150+ refereed
publications, including such journals as Nature, Nature Nanotechnology, Advanced Materials, etc., He holds 20+ patents. His current research focuses on nanomechanics
of soft material, molecules and cells; atomic force microscopy; nanophotonics and the studies towards understanding of nature of cancer, early detection
of cancer based on altered biophysical properties; self-assembly
Abstract:
Mechanics of eukaryotic cells at the nanoscale is a challenging problem due to complexity of cells. Besides fundamental
interest, such measurements are important because it has been demonstrated that the elastic modulus of cells can
correlate with various diseases and even aging. Atomic force microscopy (AFM) is the technique of use. At the same time, there
is a lot of confusion in the process of measurements of the elastic modulus of cells. In the talk, author will present the modern
overview of the topic, describe step-by-step how to do the measurements of the elastic modulus in quantitative manner that is
independent of the particular microscope, AFM probe, and mechanical model.
John B Bruning
The University of Adelaide, Australia
Title: The human sliding clamp as a therapeutic target
Biography:
John B Bruning received BSc from Texas A&M University in 1997. He began crystallography in the Laboratory of Yousif Shamoo at Rice University. During his
graduate studies he worked on the structural mechanism of the human sliding clamp and its interactions with DNA replication proteins. He received his PhD in 2005
and completed two successful Post-docs; the fi rst was at the Scripps Research Institute from 2005-2007 working on structural studies of nuclear receptors including
PPAR, RXR, ER and TR and his second Post-doc was with Jim Sacchettini in the Houston Medical Centre and as a part of the TB structural genomics consortium.
He received his fi rst faculty position at the University of Adelaide as a Lecturer in 2012. He was tenured in 2015 and promoted as Senior Lecturer in 2016. Due to
his continued collaboration with Scripps Research Institute, he was also appointed as Adjunct Professor of the Scripps Research Institute in 2016.
Abstract:
The human sliding clamp (also known as PCNA) controls access to DNA of many of the proteins involved in essential
processes such as DNA replication, DNA repair and cell cycle control. Proteins compete for interaction with the PCNA
surface by means of a short, conserved peptide sequence known as the PCNA-interacting protein motif (or PIP-box). Binding
to PCNA via the PIP box allows access to DNA. For example, the major replicative polymerase, pol delta, requires PCNA for
processive DNA synthesis, without interaction with PCNA the polymerase dissociates from DNA and is incapable of processive
DNA synthesis. As such, many groups have proposed the usefulness of PIP box mimetics for use as cancer therapeutics given
they would block upregulated PCNA form allowing interaction with pol delta and hence would inhibit DNA replication.
However, no peptide mimetics of PCNA have been forthcoming to date. Here we describe the design and synthesis of the fi rst
PCNA peptidomimetic. Our mimetic, ACR2, was designed through synthetic lactam chemistry to constrain the secondary
structure of the peptide for optimized binding to PCNA. NMR solution studies show that the wild type p21 peptide from which
ACR2 was designed adopts no defi ned secondary structure in solution, while our mimetic adopts a 310 helix in solution, which
has been shown in previous studies to be essential for PIP box binding to PCNA. Binding experiments determined a KD of 200
nM of ACR2 for PCNA, which is higher than the wild type peptide. A co-crystal structure of ACR2 bound to hPCNA revealed
the mechanism of interaction of this mimetic with PCNA.
Miki Senda
High Energy Accelerator Research Organization (KEK), Japan
Title: Crystallization strategy when no crystals are obtained in the initial screening
Biography:
Miki Senda has completed her PhD from Nagaoka University of Technology in 2008. She is an Assistant Professor of Structural Biology Research Center in High
Energy Accelerator Research Organization (KEK). She has several collaborations in which she has worked as an expert of protein crystallization and crystal quality
improvement. She received Oxford Cryosystems Low Temperature Prize at the 63rd Annual meeting of the American Crystallographic Association (ACA) in 2013.
Abstract:
Protein crystallography is an indispensable tool in the pharmaceutical and biochemical sciences. Refi nements of the protein
crystallography beam lines and their integrated programs for crystal structure analysis allow us to perform automatic or
semi-automatic structural determinations using well-diff racted crystals. However, the production of well-diff racted crystals
is still a bottleneck, even when using crystallization robots and common screening kits. Th e process of protein crystallization
does not follow a standardized, routine protocol, except in the case that good crystals are obtained at an initial crystallization
screening. In the more frequent case that no crystals or only poor crystals appear at the initial screening, there is no general
consensus regarding the next step. Nonetheless, even in the absence of well-diff racted crystals at an initial screening, it is still
possible to optimize the crystallization conditions based on the accumulated data from a wide range of protein-crystallization
attempts. Th e more such crystallization data are available, the more appropriate and effi cient optimization will be possible,
since the crystallization conditions diff er for each protein. Th erefore, at our laboratories, we are currently trying to accumulate
many experiences of protein crystallization and crystal quality improvement of poor crystals through collaboration with not
only academia but also with pharmaceutical companies. Here, we present our strategy for the effi cient generation of good
quality crystals and the successful application of our crystal quality improvement method to histone chaperone TAF-Ibeta,
the CagA oncoprotein from Helicobacter pylori and GTP sensor PI5P4Kbeta. We believe that our strategy will be applicable to
other proteins as well.
Thomas Prevenslik
QED Radiations Discovery Bay, China
Title: Protein folding and unfolding by quantum mechanics
Biography:
Thomas Prevenslik is a retired American living in Hong Kong and Berlin. Because classical physics does not work at the nanoscale, he has developed the theory of
QED radiation based on quantum mechanics. He developed the simple theory of QED based on the Planck law of QM. Differing from the complex QED by Feynman
and others, simple QED assumes any heat absorbed at the nanoscale having high surface-to-volume ratios place interior atoms under high EM confi nement that
by the Planck law of QM precludes the atoms from having the heat capacity to conserve heat by an increase in temperature. In the instant topic of protein folding
and unfolding by quantum mechanics, the atoms may only conserve heat by creating EM radiation that by removing electrons by the photoelectric effect charges
the atoms positive inducing Coulomb repulsion that enhances unfolding. On a picosecond time scale, the electrons recombine with charged atoms to place the
protein under van der Waals attraction that fold the protein. Driven by heat, protein folding, and unfolding is the consequence of fl uctuations between QM induced
charge and neutral states.
Abstract:
Proteins are sensitive to electrostatic charges from amino acid side chains that change with conformation. But molecular
dynamics (MD) simulations of protein folding and unfolding are based on classical force fi elds with electrostatic interaction
represented by fi xed point charges. Quantum mechanics (QM) modifi cation of point charges during conformational changes is
required but is impractical because of computational costs. Computation costs aside, even if point charges were continuously
updated, the eff ect on protein folding and unfolding would be insignifi cant compared to the more fundamental QM eff ect
of the Planck law on the heat capacity of atoms. In this regard, proteins are generally thought to unfold upon increasing
temperature based on the classical assumption the constituent atoms have heat capacity. But the Planck law requires the heat
capacity of the atom to vanish with conservation proceeding by creating EM radiation that by the photoelectric eff ect removes
electrons to positively charge the protein atoms. What this means is the heat thought to induce unfolding by increasing the
temperature of proteins is actually conserved by producing charge that unfolds the protein by Coulomb repulsion. To illustrate
QM induced charge, the MD simulation of folding and unfolding using for a simple 5-atom protein is illustrated in Figure 1.
Initially, the protein in the form of a semi-circle relaxes under L-J forces but does not unfold. L-J stands for Lennard-Jones.
Unfolding occurs upon applying QM induced repulsive positive charge (0.5-1 electron charges) on each atom. Folding back to
an intermediate cluster occurs by relaxing the protein with L-J forces alone without QM induced charge. Th e protein returns
to an inverted semi-circular shape by unfolding the cluster by applying the QM induced repulsive charge. How the protein
constantly modifi es QM induced charge is discussed.