Solution Structure And Constrained Molecular Dynamics Study Of Vitamin B12 Conjugates Of The Anorectic Peptide PYY(3-36)

#50, published in ChemMedChem (11 (2016), 9, 1015-1020), DOI:cmdc.201600073.

The key to molecular dynamics simulations is recycling – specifically, going into a first project with enough organization to know how to use everything in the next study. While that first successful connectivity table, parameter assignment, and RESP charge generation for something as Frankenstein-esque as vitamin B12 is the north face of Everest, that next simulation is simply a matter of having atom codes in your PDB file standardized.

And, speaking of PDBs, article #50 has the added bonus of having its own entry in the Protein Databank as 2NA5 – quite a treat (to me, anyway).

And furthermore, this is the first of my publications to benefit from the Research Computing infrastructure on the Syracuse University campus – the throughput of calculations for future work is completely unprecedented in my history of resource access anywhere (the drop in storage prices is very real to some of us).


Authors: Henry K.E., Kerwood D.J., Allis D.G., Workinger J.L., Bonaccorso R.L., Holz G.G., Roth C.L., Zubieta J., and Doyle R.P.

Abstract: Vitamin B12–peptide conjugates have considerable therapeutic potential through improved pharmacokinetic and/or pharmacodynamic properties imparted on the peptide upon covalent attachment to vitamin B12 (B12). There remains a lack of structural studies investigating the effects of B12 conjugation on peptide secondary structure. Determining the solution structure of a B12–peptide conjugate or conjugates and measuring functions of the conjugate(s) at the target peptide receptor may offer considerable insight concerning the future design of fully optimized conjugates. This methodology is especially useful in tandem with constrained molecular dynamics (MD) studies, such that predictions may be made about conjugates not yet synthesized. Focusing on two B12 conjugates of the anorectic peptide PYY(3–36), one of which was previously demonstrated to have improved food intake reduction compared with PYY(3–36), we performed NMR structural analyses and used the information to conduct MD simulations. The study provides rare structural insight into vitamin B12 conjugates and validates the fact that B12 can be conjugated to a peptide without markedly affecting peptide secondary structure.

“Upstate NY Stargazing In October” Article Posted To And

The fourth article in the series – “Upstate NY stargazing in October: Prominent constellations of summer and winter visible on Autumn nights” – is available for your reading and critical review at and The editors are still having a bit of fun with the word arrangement in the headline (I suspect the newest version was selected to get rid of the double “in” – but can’t speak to the seasonal capitalization preferences – I trust in my editors), but everything else is going fairly smoothly.


Mars to find other. Click for a larger view.

I lament the lack of any mention of the Orionid Meteor Shower, which won’t be impressive anyway thanks to the Moon, but should still have been included for monthly completeness. What would have been included in the article is provided below:

Meteor Showers: Orionids, Oct. 2 – Nov. 7, Peaking Oct. 20

Meteor showers are the result of the Earth passing through the debris field of a comet or asteroid. As these objects approach the warming sun in their long orbits, they leave tiny bits behind – imagine pebbles popping out the back of a large gravel truck on an increasingly bumpy road. In the case of meteor showers, the brilliant streaks you see are due to particles no larger than grains of sand. The Earth plows through the swarm of these tiny particles at up-to 12 miles-per-second. High in the upper atmosphere, these particles burn up due to friction and ionize the air around them, producing the long light trails we see. We can predict the peak observing nights for a meteor shower because we know when and where in Earth’s orbit we’ll pass through the same part of the Solar System – this yearly periodicity in meteor activity is what let us identity and name meteor showers well before we ever had evidence of what caused them.

The name of each meteor shower is based on the constellation from which the shooting stars appear to radiate – a position in the sky we call the radiant. In the case of the Orionids, the meteor shower radiant appears to be to the north/above of the belt and left shoulder of Orion, which rises from the east after 11 p.m. this month. The meteor shower itself is provided to us by Halley’s Comet, and is the best of the meteor showers associated with Halley’s debris field.

How to observe: Sadly, the Moon will be prominent in the late-night/early-morning sky during the days around the Orionid peak, making for a far less impressive display. The Orionids are not known for their impressive counts either, with 10 to 20 meteors per hour expected.

Orion marks the position of the meteor shower radiant, meaning the meteors themselves will seem to shoot roughly from the east to the west. To optimize your experience, lie flat on the ground with your feet pointed east and your head elevated – meteors will then appear to fly right over and around you. Counts and brightness tend to increase the later you stay out, with peak observing times usually between midnight and 4 a.m. The swarm of tiny particles is distributed broadly in orbit, meaning some people may shooting stars associated with the Orionids anytime this month.

Also, kudos to friend and fellow space trucker Prof. John McMahon for one orientational catch – the following:

Starting around mid-October, Jupiter will peak above the Western horizon just after 6:30 a.m.

should read:

Starting around mid-October, Jupiter will peak above the Eastern horizon just after 6:30 a.m.

The ability to iterate with the newspaper after providing the full content is perfectly encapsulated in a Charlie Rouse comment about Thelonious Monk in “Straight, No Chaser” – which I totally understand.

2016oct5_charlierouse“You know that you got to play correctly the first or second take or that’s it. He would take it anyhow. You mess up, well that’s it. You know, that’s your problem. You have to hear that all the rest of your life.”

For interested parties, this article also marks the second (and final) official mention (to the best of my knowledge) of our upcoming MOST/TACNY/CNYO hosting of International Observe The Moon Night on Saturday, October 8th. At present, the weather is looking less-than promising for even lunar observing, but plans are underway to handle the crowd either way.

If it rains Saturday night, then I recommend the following:

“Stargazing In Upstate NY In September” Article Posted To And

The third article in the series – “Stargazing in Upstate NY in September: Look for more subtle objects on autumn nights” – is available for your reading and critical review at and I’m pleased to report that we’ve hit our stride with the formatting and content transfer, and I can only hope the star charts make sense in their current forms.

For interested parties, this article also marks the first official mention (to the best of my knowledge) of our upcoming MOST/TACNY/CNYO hosting of International Observe The Moon Night on Saturday, October 8th. Additional details to follow, but expect the observing to happen somewhere around The MOST itself.


Extra-special thanks to Nick Lamendola from the Astronomy Section of the Rochester Academy of Science (image above, taken from the grounds of my new observing stomping grounds at the Farash Center – click for a larger view) for the use of his Perseid composite as the article opener (one of the benefits of being a member of several local clubs is the listserve content – and the many fantastic images that fly by on a weekly basis).

The Methodist Bells And Colin Phils – Highlights Of Sub Rosa Session #32 At Subcat Studios, 21 August 2016

Posting for historical purposes, given the great recording and video that came from the session.


The Methodist Bells (bandcamp facebook) had the pleasure of performing a 3/4 set on Sunday, August 21st at (my first drum teacher, Ron Keck’s) Subcat Studios for Sub Rosa Session #32. Closing for the Bells (well, I think it’s funny) was recently-US-returned-and-immediately-thereafter-Binghamton-bound Colin Phils (bandcamp facebook), who put on a fantastic trio show (and, with one of the wooden USBs in tow, I can say that their previous two albums are excellent as well).


“The band. The band. THE BAND!” Adam, me, Leah, Clem, Jeremy, et Maurice.

Alice In The Sky, featuring an Allis On The Ground

With thanks to Amanda Rogers for organizing, Subcat, The Rebel 105.9 (we don’t get it in Rochester, though), The Syracuse New Times, D.I.T. Records, and my current contributing writer hosters at for making the session and recording possible, a video work-up of “Alice In The Sky” is provided below for your viewing and listening pleasure (courtesy

On day two of an 11-hour jet lag, hadn’t played in a month, stuck behind a poorly-left-ified kit, and still sound good.

The Colin Phils tune “Don Cabs” is included below. I was (admittedly) ready to sneak out early, but ended up staying for the whole set (that’s musician-speak for “great show”).


Our fearless leader Clem Coleman (twitter facebook) was featured in a recent Daily Orange article, in which I make my third (known) appearance in the DO ever since starting at SU in 1994.


PDF (local, for posterity): 2016sept7_methodistbells_dailyorange.pdf

“Stargazing In Upstate New York” – Links To The First Two Columns At And

Free press all around,

In the interest of aggregation, quick post linking the first two in a new series of astronomy articles on and There’s an old adage in academia – “You don’t really know something until you can teach it.” To that end, these articles and their associated research prep are great fun and yet another excellent excuse to go out at night and compare the planetarium apps to the real thing (for which both Starry Night Pro and Stellarium are excellent organizational proxies. I’m currently leaning on Stellarium for the imagery because others who might get bit by the astronomy bug can download it for free and follow along. That said, Starry Night Pro is still my workhorse for fine detail as Stellarium continues to develop).


When the article series was first proposed, the goal for the Syracuse Media Group folks was to provide people in upstate some basic information for what was up and about in the night sky – when you step outside, what’s there to find? My hope is to provide the non-observer and novice observer just enough information to whet the appetite, hopefully coaxing readers to take some quality looks and, if all goes well, to seek out their local astronomy club for some serious observing – and learning.

Night sky-gazing in Upstate NY: What to look for in July

– article @…_look_for_in_july.html

– article @…_look_for_in_july.html

Introducing the article organization, with first looks, spotting the International Space Station (ISS), moon phases, visible planets, and a constellation-a-month identifier to close it all.

Stargazing in Upstate NY in August: See the Milky Way, Perseid meteor shower

– article @…_meteor_shower.html

– article @…_meteor_shower.html

The series started just in time to highlight the Perseid Meteor Shower (and get its first linking to thanks to Glenn Coin’s article as we approached the Perseid peak), then August was chock full of interesting planetary events. The August article was also a first exposure to the issues of episodic astronomy – how to be as minimally referential as possible in any single article to previous articles (which is not easy given how much the search for constellations historically has involved the finding of a bright one to orient observers to a dimmer one).

July hit 78 shares on, August hit 4400 – at that rate, the whole world will see the October article.

Peptide Springiness By Terahertz Spectroscopy – An Upcoming Cover For Angewandte Chemie (And A POV-Ray File For Generating Springs)



Image caption: An approach combining terahertz spectroscopy, X-ray diffraction, and solid-state density functional theory was utilized to accurately measure the elasticities of poly-l-proline helices by probing their spring-like vibrational motions. In their communication (DOI: 10.1002/anie.201602268), T. M. Korter and co-workers reveal that poly-l-proline is less rigid than commonly expected, and that the all-cis and all-trans helical forms exhibit significantly different Young’s moduli.


Continue reading “Peptide Springiness By Terahertz Spectroscopy – An Upcoming Cover For Angewandte Chemie (And A POV-Ray File For Generating Springs)”

More On The Virtues Of VirtualBox – ACID (or AICD) Under Ubuntu 14.04 (By Way Of OpenSuse 11.2)

“Stop that!” – George Carlin

If you’ve obtained source code from an academic lab that was last developed some time ago and you spent a whole day installing libraries and symbolic links and redefining variables in your .bashrc and downgrading libraries and redefining paths and have 20 tabs open in your browser that all go to 20 different obscure error discussions on Stack Overflow and it’s late and you’re tired and you think you might not need the program after all if you do a bunch of other workaround things instead – what’s below is for you.

Academics have been developing small code for (nearly) millions of years to make their lives easier – and we all benefit when that code is made available to others (esp. when it helps in data analysis). When that code is a series of perl or python scripts, there’s generally little reason why you should have any run issues. When they call on external libraries or specific tools, generally that information is available in the README somewhere. Generally speaking, there’s no reason why a code shouldn’t work in a straightforward manner when the developer doesn’t make it known that something else needs be installed to make it work.

So, why doesn’t code A work on your linux box? A few possibilities.

Continue reading “More On The Virtues Of VirtualBox – ACID (or AICD) Under Ubuntu 14.04 (By Way Of OpenSuse 11.2)”

OrthoDB 1.6 Installation On Ubuntu 14.04 (And Related) – Build Errors And The Simple Fixes

UPDATE: 20 May 2016 – With thanks to OrthoDB’s very own Fredrik Tegenfeldt, here’s a more distro-complete fix for the Makefile.rules file.

# BRH flags
ifeq ($(USE_BRH),1)
BRH_DIR        = $(BASE_DIR)
CPPFLAGS    += -I$(BRH_DIR)/src
ifeq ($(WITH_RPATH),1)
LDFLAGS        += -L$(LIB_DIR) -Wl,-rpath,$(LIB_INSTDIR)
LDFLAGS        += -L$(LIB_DIR)
LDLIBS        += -lbrh

ifeq ($(USE_BOOST_THREAD),1)
LDFLAGS        += -pthread
LDLIBS      += -L$(DIR_BOOST_LIB) -lboost_system -L$(DIR_BOOST_THREAD) -l$(LIB_BOOST_THREAD) -lpthread

And Happy New Year,

Yet another random Ubuntu-centric bioinformatics aside in the event others run into the same build issues (with errors included below, as you likely googled those first). For those wondering…

The Hierarchical Catalog of Orthologs v8

Orthology (website, download) is the cornerstone of comparative genomics and gene function prediction. OrthoDB aims to classify protein-coding genes from the increasing number of available sequenced genomes into groups of orthologs descended from a single gene of the last common ancestor (LCA) of each clade of species. Applying this concept to the hierarchy of LCAs along the species phylogeny results in multiple levels of orthology: the more closely-related the species, the more finely-resolved the orthologous relations.

The build here was on a fresh installation of 64-bit Ubuntu 14.04 (Trusty Tahr). All of the errors produced come from running on that clean install, meaning you’ll run into dumb errors (like missing build-essential), didn’t-know-we-needed-that errors (boost), and that’s-probbly-an-Ubuntu-oddity errors (with a modified Makefile.rules file with explicit boost calls linked to below; I suspect the developers are working on a non-Ubuntu distro).

Continue reading “OrthoDB 1.6 Installation On Ubuntu 14.04 (And Related) – Build Errors And The Simple Fixes”

Some Recent WordPress Theme Hacking Issues (Mass Emails To Non-Existent Domain Name Addresses) And A Couple Of Things To Look For

I’ve spent the past few weeks making several new email client filters each day, with subject lists that look like the following:

Saturday and Sunday Only! Today’s Special Buy of the Day!

One day sale event – today only, [ insert date here ]

[ insert name here ], check out this weeks specials – up to 75% off on selected items

[ Insert name here ], 10% discount for Brand or Generics for purchases placed before [ insert date here ]

We appreciate your past business with us

[ insert name here ], some of your items are back in stock now – complete your order today

[ insert date here ] deals and savings from your supplier

Continue reading “Some Recent WordPress Theme Hacking Issues (Mass Emails To Non-Existent Domain Name Addresses) And A Couple Of Things To Look For”

Private Internet Access, OpenVPN (2.3.2), and Ubuntu 14.04 (.2 LTS) – Yet Another Reported Way To Get Them Working (And The Only One That Works For Me)

Update: 17 May 2016 – Doesn’t happen often and is always nice to see. Thanks to Lucas Nell (on 26 April – that’s my bad) for taking one additional step out of the whole process with the script below. Simply replace “[put-your-password-here]” with your actual password (and no brackets), same the below as some_name.script (or whatever), chmod +x some_name.script to make it official, and you’re good to go to make the additional mod.

sudo -s

cd /etc/NetworkManager/system-connections

export pwd="\n[vpn-secrets]\npassword=[put-your-password-here]"

for f in PIA*
  sed -i 's/password-flags=1/password-flags=0/g' "${f}"
  echo -e "${pwd}" >> "${f}"


If you sign up for an account with Private Internet Access (and this may go for some other VPN providers as well) and follow the only prominent Ubuntu link (12.04) in the Support Section (, you’ll be taken to a reasonably straightforward 9-step process that walks you through the OpenVPN setup – from the script download to the selection of PIA-points (I just made that up) in your Network Manager GUI (that radial wifi icon or arrows in the upper-right corner).

That is, for Ubuntu 12.04.

The Problem

If you try this in Ubuntu 14.04, everything more-or-less looks and runs the same way. That said, when you try to connect to a PIA-point in the Network Manager, nothing happens. Your wifi radial doesn’t change, flash, or provide any indication that something has gone right or wrong. More importantly (to the lack of feedback, anyway), you are not asked for your PIA password (having put in your username in the install process). This lack of password requesting turns out to be the real kicker (and diagnostic for the fix presented down below).

Continue reading “Private Internet Access, OpenVPN (2.3.2), and Ubuntu 14.04 (.2 LTS) – Yet Another Reported Way To Get Them Working (And The Only One That Works For Me)”