Ryan M B Hoffman- PhD, Guild Certified Feldenkrais Practitioner
- Self-employed
Ryan M B Hoffman
- PhD, Guild Certified Feldenkrais Practitioner
- Self-employed
About
29
Publications
26,432
Reads
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1,402
Citations
Introduction
I'm mostly interested in the role of protein conformational fluctuations in biological processes. I've mostly worked as an experimental structural biologist but I have interests in theoretical biology. I prefer to work with insects as model organisms, and I would like to address the delineation of structure-function relationships at both the molecular and whole-organism scales, and in the context of evolutionary biology.
Current institution
Self-employed
Additional affiliations
September 2017 - December 2017
Hope College, Drumheller
Position
- Intructor
Description
- Introductory Biochemistry in a community college setting.
April 2016 - April 2016
Position
- Lecturer
Description
- I presented "An Introduction to the Feldenkrais Method" to a class of Massage Therapy students.
May 2016 - August 2016
Position
- Instructor
Description
- BIOL 12 is an introductory Biology course with lab. I lectured and instructed the labs.
Education
May 2012 - May 2016
Feldenkrais Institute of San Diego
Field of study
- Feldenkrais Method of Somatic Education
May 2002 - November 2008
September 1998 - May 2002
Publications
Publications (29)
Various intrinsic disorder (ID) prediction algorithms were applied to the three tissue isoforms of troponin I (TnI). The results were interpreted in terms of the known structure and dynamics of troponin. In line with previous results, all isoforms of TnI were predicted to have large stretches of ID. The predictions show that the C-termini of all is...
Durable influenza protection
Vaccines are indispensable for the control and prevention of influenza, but there are several challenges to efficacy. Some individuals respond poorly to vaccination, and virus variation makes targeting optimal antigens difficult. Broadly neutralizing antibodies are one solution, but they have their own pitfalls, includi...
Flu vaccine candidate STEMs the tide
Every year we need a new flu vaccine, because influenza virus constantly mutates the major target of antibodies to flu: the “head” region of the viral hemagglutinin (HA) protein. Avoiding the problem of mutation requires a vaccine that elicits antibodies against the more conserved “stem” region of HA. During inf...
In his 1951 Lane Medical Lectures, Kaj Ulrich Linderstrom-Lang (LL) organized protein structure into a three-tiered hierarchy, with the amino acid sequence comprising the primary structure, local-in-sequence interactions stabilizing the secondary structure, and long-range interactions stabilizing the tertiary structure. Here we call this ‘the LL on...
Unlabelled:
Due to continuous changes to its antigenic regions, influenza viruses can evade immune detection and cause a significant amount of morbidity and mortality around the world. Influenza vaccinations can protect against disease but must be annually reformulated to match the current circulating strains. In the development of a broad-spectru...
Significance
The HA surface glycoprotein on influenza A viruses mediates viral entry into host cells. HA is highly variable and classified into 18 divergent subtypes, which cluster into two major phylogenetic groups. Antibody CR8043 has heterosubtypic neutralizing activity against group 2 viruses, including H3 viruses that currently circulate in hu...
Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in antigenicity, but fortunately was not nearly as deadly. 5J8 is a human antibody that potently neutralizes a broad spectrum of H1N1 viruses, including the 1918...
A novel panel of influenza vaccines contain modules that target both the innate and adaptive immune system on a continuous polypeptide. These modules produce a more immunogenic vaccine than if they are co-administered as separate molecules. The immunogenicity also varies with the particular arrangement (and stoichiometry) of modules in the construc...
A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a se...
A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a se...
The analysis of kinetic and thermodynamic data measured at single residue level, and the perturbation produced by mutagenesis or denaturant agents, may be useful for tuning simulation parameters, and provide a precise description of proteins structural dynamics. Phi value and hydrogen exchange are some of the experimental techniques that provide th...
The mechanistic interpretation of continuous molecular dynamics time series faces well-understood challenges, primarily obtaining a statistically significant number of folding trajectories under a sufficiently accurate force field. To avoid some of these limitations, here we use discontinuous sampling over the folding reaction coordinate (umbrella...
Simulations based on perfectly funneled energy landscapes often capture many of the kinetic features of protein folding. We examined whether simulations based on funneled energy functions can also describe fluctuations in native-state protein ensembles. We quantitatively compared the site-specific local stability determined from structure-based fol...
Simulations based on perfectly funneled landscapes have been able to capture many of the fundamental aspects of protein folding. When frustration is low enough the topology becomes the main factor determining the folding process. In the most fundamental implementation of the minimal frustration principle only native interactions significantly contr...
The IkB proteins, inhibitors of the transcription factor NF-kB, are comprised of tandem repeats of a conserved primary structure. The tandem repeats are stabilized as a repeated tertiary structural motif, at least when complexed with NF-kB and DNA. Structural fluctuations in the native state deviate substantially from a simple repeating pattern, as...
The calmodulin antagonist W7 binds to troponin C in the presence of Ca(2+) and inhibits striated muscle contraction. This study integrates multiple data into the structure of the regulatory domain of human cardiac troponin C (cNTnC) bound to Ca(2+) and W7. The protein-W7 interface is defined through a three-dimensional {(1)H,(13)C}-edited-{(1)H,(12...
cTnC-cTnI interaction plays a critical role in transmitting the Ca2+-signal to the other myofilament proteins in heart muscle contraction. As such, the cTnC-cTnI interface constitutes a logical target for cardiotonic drugs that can modulate the Ca2+-sensitivity in cardiomyocytes. We have shown that W7, a calmodulin antagonist, binds specifically to...
The flycasting mechanism for troponin, as proposed by Tharin Blumenschein, and developed by Ryan Hoffman and Brian Sykes. Major contributions for this animation are due to Jocelyn Dombroski.
Intrinsic disorder (ID) prediction algorithms were used to assess the distribution and extent of ID in the three tissue isoforms of troponin I (TnI). Consistent with previous experimental findings in the fast skeletal system, all prediction approaches identi- fied the termini as intrinsically disordered. The N-terminal extension unique to the cardi...
When Galvani discovered the electrical regulation of muscle contraction science began an inexorable transformation. Observation of an inorganic trigger for a physiological event presaged the end of vitalism, the beginning of electrochemistry, and over 400 years of research into the first demonstrable biochemical machine: striated muscle. This molec...
TnI 96–182 (CTnI) TnI 131–182 the mobile domain (Md) } TnI 114–133: a fragment containing C'-inhibitory region and the switch peptide (Ip-Sp) TnI TnT TnC } ABSTRACT The troponin (Tn) complex transduces Ca 2+ fluctuations into conformational changes which transition the thin filament between contraction-inhibited and contraction-competent states. Re...
W7 is a well-known calmodulin (CaM) antagonist and has been implicated as an inhibitor of the troponin C-mediated Ca(2+) activation of cardiac muscle contraction. In this study, we use NMR spectroscopy to study binding of W7 to cardiac troponin C (cTnC) free or in complex with cardiac troponin I (cTnI) peptides. Titration of cTnC.3Ca(2+) with W7 sh...
The troponin (Tn) complex regulates the thin filament of striated muscle by transducing [Ca²⁺] fluctuations into conformational changes. These changes propagate to tropomyosin (Tm), which then assumes a new disposition with respect to actin, reversibly exposing actin's binding sites for the thick filament motor-ATPase (myosin). To date, the structu...
W7 is a well-characterized calmodulin antagonist. It decreases the maximal tension and rate of ATP hydrolysis in cardiac muscle fibers. Cardiac troponin C (cTnC) has been previously implicated as the mechanistically significant target for W7 in the myofilament. Two-dimensional NMR spectra ({1H,15N}- and {1H,13C}-HSQCs) were used to monitor the Ca2+...
We describe the binding of W7, a small molecule inhi- bitor, to Ca-loaded cardiac troponin C (cTnC). W7 is a well-characterized
calmodulin (CaM) antagonist. It decreases the maximal tension and rate of ATP hydrolysis in cardiac muscle fibers [Adhikari BB, Wang K. Biophys J. 86:359-70 (2004)]. cTnC has been implicated as the mechanistically signific...
Questions
Questions (3)
This question can be broadened to the most of the physical sciences and mathematics, but I'm mostly interested in chemistry concepts like 'bonding' and 'structure.' At which age can a particular concept be assimilated? I'm not an education theorist; please feel free to suggest appropriate background reading. I'm expecting the answer is contextualized on the dominant educational approach for a given culture.
I'm currently reading Gillott's "Entomology" and I want an alternative approach to the basic anatomy and physiology. Any thoughts on Snodgrass' "Principles of Insect Morphology" for example?
Recommended so far:
•Insects structure and function, 5th edition. RJ Chapman (suggested by Barkat Hussain, Khalid Ali Khan, Arash Zibaee, Ravi Kant Upadhyay, Konstantinos B. Simoglou).
•Insect Physiology and Biochemistry 2th edition. James L. Nation (suggested by Arash Zibaee).
•The Insects: An Outline of Entomology, 4th Edition. P.J. Gullan and P.S. Cranston (suggested by Steven J. R. Allain, Kambiz Esfandi, Pavel Jakubec).
•Physiological systems in insects. M.J. Klowden. (suggested by Konstantinos B. Simoglou)
•Insect-plant biology, 2nd ed. Schoonhoven, L.M., J.J.A. van Loon and M. Dicke. (suggested by Konstantinos B. Simoglou, Pavel Jakubec)
•The Science of Entomology. William S Romoser and John G Stoffolano Jr (suggested by Munir Ahmad).
•Fundamentals of Entomology. Richard J Elzinga (suggested by Munir Ahmad).
•Ecology of Insect: Concepts and Applications, Speight M.R., Hunter M.D. & Watt A.D. (suggested by Pavel Jakubec)
