README for Electronic Appendices to Simmonds, Anna L 2021 thesis 'Elucidating the structural consequences of phosphorylation by mass spectrometry, ion mobility and molecular modelling

Grant Number: EP/L013646/1

Project Title: ELUCIDATING THE STRUCTURAL CONSEQUENCES OF PHOSPHORYLATION BY MASS SPECTROMETRY, ION MOBILITY AND MOLECULAR MODELLING

List of files:
1-1_gesptoooff_code.txt
1-2_MS_ff_parameters
1-3_IMoS_input.cla
1-4_kmeans_opt.m
1-5_solariX_XR_instrument_parameters.xlsx
1-6_Synapt_G2S_instrument_paramters.xlsx
1-7_14-3-3-z_clustering_information.xlsx
1-8_14-3-3-z_non-covalent_interactions.xlsx
1-9_GSK3B_clustering_information.xlsx
1-10_GSK3B_non-covalent_interactions.xlsx
1-11_GSK3B-z17_clustering_information.xlsx
1-12_GSK3B-z17_non-covalent_interactions.xlsx
1-13_Bcasein-c28_clustering_information.xlsx
1-14_Bcasein-c28_non-covalent_interactions.xlsx
1-15_Representative_structures


Description of each file:
1-1_gesptoooff_code.txt
	A bash script that converts .gesp files that describe the electrostatic potential of a Ac-Gly and Gly-Am capped amino acid residue produced by Gaussian 09 and converts it to a .off file for use in AMBER16
	Dependencies: AMBER16 (prepgen, parmchk2, tleap)
	Script is optimised for use on bluebear linux HPC, but works in any bash shell with AMBER installed
	Reads in a set of ???_filename.gesp (where ??? is a three letter amino acid code) and converts them to a set of .prepi residues called ?res-name (where ? is a single letter amino acid code to identify the amino acid and res-name is a 2 letter string to identify the characteristics of the set) then converts them to a .off library for the whole set 
	If ??? is not recognised as a three letter amino acid code the residue will be saved as res-name.prepi
	Useage: ./gesptooff filename res-name res-type-"mid"-"C"-or"N" .off-name
	
1-2_MS_ff_parameters
	A folder containing .off and .frcmod files created in Ubuntu 14.04 using the gesptooff_code.txt script for amino acid residues parameterised in this work by optimisation in Gaussian09 (HF 6-31G (d,p)), and calculation of the electrostatic potential using the Merz-Singh-Kollman scheme
	Residues are intended to used in AMBER with the ff99sb and phos10aa forcefields
	Residue sets:
		Netural Arginine:
			neutral_Arg.off, Arg_neutral_GlyAcNT_GlyAmCT.frcmod
		Residues adjacent to c fragment cleavage site:
			c_pos.off
		Cysteine-S-acetamide:
			CAM.off, CAM.frcmod
		Neutral C-terminal residues:
			nCT_atbb.off, nCT_frcmod
		Neutral N-terminal residues:
			nNT_atbb.off, nNT_frcmod
		Neutral phosphoserine:
			S0P.off, S0P.frcmod
		Neutral phosphotyrosine:
			Y0P.off, Y0P.frcmod
		Residues adjacent to z fragment clevage site:
			z_radical.off, z_radical_frcmod

1-3_IMoS_input.cla
	Example IMoS input text file detailing the parameters used for ion mobility calculation (TMLJ method) of a .pdb file containing 1000 molecular models
	Intended for use with IMoS as a command line tool in Ubuntu 14.04

1-4_kmeans_opt.m
	MATLAB code for ensemble analysis of CCS-matched molecular modelling ensembles
	Ensembles are read in as .txt files of atomic coordinates, with a .pdf file for one structure of the ensemble used to give atom identites for the molecule
	Molecular models are converted to a vector of pairwise distances between all atoms, followed by random projection of the ensemble, t-SNE and k-means clustering of the projections, and calculation of distances between acidic and basic residues in the structures closest to the centroid of each cluster
	Cluster information and distances between acidic and basic residues are saved to a .xlsx file

1-5_solariX_XR_instrument_parameters.xlsx
	Instrument parameters used during all experiments performed on solariX XR mass spectrometers:
		ESI method
		Potential / V
		Temperature / ◦C
		Exit potential / V
		Deflector / V
		Potential / V
		RF amplitude / Vpp
		Mass
		Q width / m/z
		Collision voltage / V
		DC extract bias / V
		RF frequency / MHz
		RF amplitude / Vpp
		Collision gas flow / %
		Reagent mass
		Reagent accumulation / ms
		Reaction time / ms
		Mirror RF amplitude / Vpp
		Time of flight / s
		RF frequency / MHz
		RF amplitude / Vpp
		Ion accumulation / s
		Transfer exit lens / V
		Analyser entrance / V
		Side kick / V
		Side kick offset / V
		Front trap plate / V
		Back trap plate / V
		Back trap plate quench / V
		Sweep power / dB
		DC bias RX0 / V
		DC bias TX180 / V
		DC bias RX180 / V
		DC bias TX0 / V
		ICR cell fills
		Mass / m/z
		Sweep power / %
		Notch width / m/z
		Time delay / s
		Bias
		Lens
		Pulse length / s
		MS^3 pulse length / s


1-6_Synapt_G2S_instrument_paramters.xlsx
	Instrument parameters used during all experiments performed on Synapt G2S mass spectrometers
		Lteff
		Veff
		Resolution
		Min Points in Peak
		Acquisition Device
		Acquisition Algorithm
		ADC Trigger Threshold (V)
		ADC Input Offset (V)
		Average Single Ion Intensity
		ADC Amplitude Threshold
		ADC Centroid Threshold
		ADC Ion Area Threshold
		ADC Ion Area Offset
		ADC Pushes Per IMS Increment
		EDC Delay Coefficient
		EDC Delay Offset
		Polarity
		Capillary (kV)
		Discharge Current (uA)
		Source Temperature (°C)
		Sampling Cone
		Source Offset
		MakeUp Gas Flow (mL/min)
		Desolvation Temperature (°C)
		Cone Gas Flow (L/Hr)
		Nanoflow Gas Pressure (Bar)
		Purge Gas Flow (mL/h)
		Desolvation Gas Flow (L/Hr)
		Nebuliser Gas Flow (Bar)
		LM Resolution
		HM Resolution
		Aperture 1
		Pre-filter
		Ion Energy
		Manual Trap Collision Energy
		Trap Collision Energy
		Manual Transfer Collision Energy
		Transfer Collision Energy
		Manual Gas Control
		Trap Gas Flow (mL/min)
		Transfer Gas Flow (mL/min)
		IMS Gas Flow (mL/min)
		HeliumCellGasFlow
		Detector
		DetectorCache
		Acceleration1
		Acceleration2
		Aperture2
		Transport1
		Transport2
		Steering
		Tube Lens
		Pusher
		Pusher Offset
		Puller
		Pusher Cycle Time (µs)
		Pusher Width (µs)
		Collector
		Collector Pulse
		Stopper
		Stopper Pulse
		Entrance
		Static Offset
		Puller Offset
		Reflectron Grid (kV)
		Flight Tube (kV)
		Reflectron (kV)
		Use Manual Trap DC
		Trap DC Entrance
		Trap DC Bias
		TrapGate
		Trap DC
		Trap DC Exit
		Use Manual IMS DC
		IMS DC Entrance
		Helium Cell DC
		Helium Exit
		IMSBias
		IMS DC Exit
		USe Manual Transfer DC
		Transfer DC Entrance
		Transfer DC Exit
		Trap Manual Control
		Trap Wave Velocity (m/s)
		Trap Wave Height (V)
		IMS Manual Control
		IMS Wave Velocity (m/s)
		Transfer Manual Control
		Transfer Wave Velocity (m/s)
		Transfer Wave Height (V)
		Step Wave 1 In Manual Control
		Enable Reverse Operation
		Step Wave 1 In Velocity (m/s)
		Step Wave 1 In Height
		Step Wave 1 Out Manual Control
		Step Wave 1 Out Velocity (m/s)
		Step Wave 1 Out Height
		Step Wave 2 Manual Control
		Step Wave 2 Velocity (m/s)
		Step Wave 2 Height
		Use Manual Step Wave DC
		Step Wave TransferOffset
		Step Wave DiffAperture1
		Step Wave DiffAperture2
		Use Automatic RF Settings
		StepWave1RFOffset
		StepWave2RFOffset
		Target Enhancement Enabled
		Target Enhancement Mode
		Target Enhancement Mass
		Target Enhancement Trap Height (V)
		Target Enhancement Extract Height (V)
		Using Mobility Delay after Trap Release
		IMS Wave Delay (µs)
		Backing
		Source
		Sample Plate
		Trap
		Helium Cell
		IMS
		Transfer
		TOF
		IMSRFOffset
		IMSMobilityRFOffset
		TrapRFOffset
		Use Automatic RF Settings
		StepWave1RFOffset
		StepWave2RFOffset
		TransferRFOffset
		MS Profile Type
		MSProfileMass1
		MSProfileDwellTime1
		MSProfileRampTime1
		MSProfileMass2
		MSProfileDwellTime2
		MSProfileRampTime2
		MSProfileMass3
		PusherInterval
		PusherOffset
		LockMassValidSigma
		Acquisition mass range
		Start mass
		End mass
		Calibration mass range
		Start mass
		End mass
		Scan Time (sec)
		Interscan Time (sec)
		Set Mass
		Start Mass
		MSMS End Mass
		Start Time (mins)
		End Time (mins)
		Data Format
		Analyser
		ADC Sample Frequency (GHz)
		ADC Pusher Frequency (µs)
		ADC Pusher Width (µs)
		Use Tune Page Cone Voltage
		Using Auto Trap Collision Energy (eV)
		Use Auto Transfer Collision Energy
		Sensitivity
		Dynamic Range
		Save Collapsed Retention Time Data
		Use Rule File Filtering
		FragmentationMode
		Calibration
		Refill SetMass
		Refill Scan Interval Time
		Refill Scan Time

1-7_14-3-3-z_clustering_information.xlsx
	Information on clusters produced using kmeans_opt.m for 14-3-3-z peptides as a Microsoft Excel spreadsheet

1-8_14-3-3-z_non-covalent_interactions.xlsx
	Information on non-covalent interaction distances produced using kmeans_opt.m for 14-3-3-z peptides as a Microsoft Excel spreadsheet

1-9_GSK3B_clustering_information.xlsx
	Information on clusters produced using kmeans_opt.m for GSK3B peptides as a Microsoft Excel spreadsheet

1-10_GSK3B_non-covalent_interactions.xlsx
	Information on non-covalent interaction distances produced using kmeans_opt.m for GSK3B peptides as a Microsoft Excel spreadsheet

1-11_GSK3B-z17_clustering_information.xlsx
	Information on clusters produced using kmeans_opt.m for GSK3B-z17 fragments as a Microsoft Excel spreadsheet

1-12_GSK3B-z17_non-covalent_interactions.xlsx
	Information on non-covalent interaction distances produced using kmeans_opt.m for GSK3B-z17 fragments as a Microsoft Excel spreadsheet

1-13_Bcasein-c28_clustering_information.xlsx
	Information on clusters produced using kmeans_opt.m for Bcasein-c28 fragments as a Microsoft Excel spreadsheet

1-14_Bcasein-c28_non-covalent_interactions.xlsx
	Information on non-covalent interaction distances produced using kmeans_opt.m for Bcasein-c28 fragments as a Microsoft Excel spreadsheet

1-15_Representative_structures
	A folder containing .pdb files for all representative structures (those closest to the centroid of the clusters produced by the kmeans_opt.m script) for all 14-3-3-z, GSK3B, GSK3B-z17 and Bcasein-c28 peptides and fragments

Publications: https://doi.org/10.1021/acs.jpcb.9b08506