Cytoskeletal signaling: is memory encoded in microtubule lattices by CaMKII phosphorylation?
Open accessAbstract
Memory is attributed to strengthened synaptic connections among particular brain neurons, yet synaptic membrane components are transient, whereas memories can endure. This suggests synaptic information is encoded and 'hard-wired' elsewhere, e.g. at molecular levels within the post-synaptic neuron. In long-term potentiation (LTP), a cellular and molecular model for memory, post-synaptic calcium ion (Ca²⁺) flux activates the hexagonal Ca²⁺-calmodulin dependent kinase II (CaMKII), a dodacameric holoenzyme containing 2 hexagonal sets of 6 kinase domains. Each kinase domain can either phosphorylate substrate proteins, or not (i.e. encoding one bit). Thus each set of extended CaMKII kinases can potentially encode synaptic Ca²⁺ information via phosphorylation as ordered arrays of binary 'bits'. Candidate sites for CaMKII phosphorylation-encoded molecular memory include microtubules (MTs), cylindrical organelles whose surfaces represent a regular lattice with a pattern of hexagonal polymers of the protein tubulin. Using molecular mechanics modeling and electrostatic profiling, we find that spatial dimensions and geometry of the extended CaMKII kinase domains precisely match those of MT hexagonal lattices. This suggests sets of six CaMKII kinase domains phosphorylate hexagonal MT lattice neighborhoods collectively, e.g. conveying synaptic information as ordered arrays of six "bits", and thus "bytes", with 64 to 5,281 possible bit states per CaMKII-MT byte. Signaling and encoding in MTs and other cytoskeletal structures offer rapid, robust solid-state information processing which may reflect a general code for MT-based memory and information processing within neurons and other eukaryotic cells.
AI snapshot
Written from the paper’s full text.
TL;DR
The paper proposes that activated CaMKII holoenzymes can bind microtubule lattices and encode synaptic information as ordered phosphorylation patterns, with geometry and electrostatics matching hexagonal tubulin arrays. It estimates capacities of 64, 729, or 5,281 states per CaMKII–MT neighborhood and argues this could provide a robust, low-cost molecular memory code.
Key findings
- Activated CaMKII’s six extended kinase domains geometrically match MT A- and B-lattice hexagonal tubulin neighborhoods; the CaMKII hexagon is approximately 20 nm in breadth, and A-lattice matching is precise, while B-lattice matching requires slightly greater linker flexibility.
- Electrostatic complementarity yields an estimated attraction of 10 kT (6 kcal/mol) per kinase–tubulin monomer interaction, up to 60 kT (36 kcal/mol) when all six kinase regions are involved.
- Each kinase can convey one bit (phosphorylation vs. no phosphorylation), so six kinases can act as a 6-bit “byte”; the paper calculates 64 possible states for binary A-lattice patches, 729 states for ternary A-lattice patches, and 5,281 states for ternary B-lattice patches.
- Maximal encoding across the brain is estimated at 10^19 ATP/second, about 2% of the brain’s total energy consumption, and the authors suggest phosphorylation patterns could regulate C-terminal tail states, MAP attachment, motor protein transport, signaling, and Boolean logic gates.
Methods
- Computational molecular modeling and electrostatic profiling, not experimental wet-lab work.
- Homology models of human αCaMKII domains were built using MODELLER 9V6 with PDB templates 1HKX and 2VZ6; tubulin models used repaired PDB 1JFF/1TUB and templates for TUBA1A and TUBB3.
- MT A- and B-lattice structures were built in PyMOL using published MT geometry; electrostatics were analyzed with PROPKA/PDB2PQR and APBS Poisson-Boltzmann calculations at <1 Å grid spacing, with isosurfaces at ±0.5 kT/e.
Limitations
- The paper states no formal limitations section.
- Evident from the text: the work is purely computational/theoretical, with no experimental validation of CaMKII–MT binding, phosphorylation patterns, or memory encoding.
- Evident from the text: the exact CaMKII phosphorylation site(s) on tubulin are unknown, and the information-capacity scenarios are explicitly hypothetical.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
0 of 16 cited sources checked · 0 supported · 0 flagged
- Findingreasoning
The total number of possible states for the B lattice neighborhood is 5281 unique states.
“The total number of possible states for the B lattice neighborhood is thus 36–28−8(27) = 5281 unique states.”
Quote in the paperSubstantial claim- The authors state this as an assumption: Each extended kinase can either phosphorylate at the S-T site on a tubulin substrate, or not.
- Findingreasoning
Six possible sites on the A-lattice yield 3^6 = 729 possible states.
“Six possible sites on the A-lattice yield 36 = 729 possible states.”
Quote in the paperSubstantial claim- The authors state this as an assumption: Each extended kinase can either phosphorylate at the S-T site on a tubulin substrate, or not.
- Findingown data
The electrostatic pattern of tubulin dimers on a MT surface is complementary to that formed by the 6 CaMKII holoenzyme kinase domains.
“These electrostatic fingerprints are complementary to those formed by the 6 CaMKII holoenzyme kinase domains making the two natural substrates for interaction.”
Quote in the paperSubstantial claim - Findingown data
Spatial dimensions and geometry of the extended CaMKII kinase domains precisely match those of MT hexagonal lattices.
“Using molecular mechanics modeling and electrostatic profiling, we find that spatial dimensions and geometry of the extended CaMKII kinase domains precisely match those of MT hexagonal lattices.”
Quote in the paperSubstantial claim - Findingown data
There are two plausible sites for direct phosphorylation of tubulin by a CaMKII kinase domain.
“We also demonstrate two plausible sites for direct phosphorylation of tubulin by a CaMKII kinase domain, and calculate binding energies in the range of 6 to 36 kcal/mol per CaMKII-tubulin phosphorylation event.”
Quote in the paperSubstantial claim
- Findingown data
Binding energies for CaMKII-tubulin phosphorylation events are in the range of 6 to 36 kcal/mol.
“We also demonstrate two plausible sites for direct phosphorylation of tubulin by a CaMKII kinase domain, and calculate binding energies in the range of 6 to 36 kcal/mol per CaMKII-tubulin phosphorylation event.”
Quote in the paperSubstantial claim - Findingown data
CaMKII size and geometry of 6 extended kinase domains precisely match hexagonal arrays of tubulin in both A-lattice and B-lattices.
“We find that CaMKII size and geometry of 6 extended kinase domains precisely match hexagonal arrays of tubulin in both A-lattice and B-lattices.”
Quote in the paperSubstantial claim - Interpretationown data
Clusters of phosphorylated tubulin and/or MAP attachment may serve as logic gates for propagating information.
“Clusters of phosphorylated tubulin, and/or MAP attachment may serve as logic gates for propagating information.”
Quote in the paperSubstantial claim - Interpretationreasoning
Sets of six CaMKII kinase domains phosphorylate hexagonal MT lattice neighborhoods collectively.
“This suggests sets of six CaMKII kinase domains phosphorylate hexagonal MT lattice neighborhoods collectively”
Quote in the paperSubstantial claim - Interpretationreasoning
CaMKII phosphorylation of post-synaptic protein substrates is a likely mechanism for memory encoding/storage and regulation of synaptic plasticity.
“CaMKII phosphorylation of post-synaptic protein substrates is a likely mechanism for memory encoding/storage and regulation of synaptic plasticity.”
Quote in the paperSubstantial claim - Interpretationreasoning
Subsequent phosphorylation by CaMKII of a particular substrate may encode memory, for example as ordered arrays of 6 bits (one byte).
“As CaMKII activation represents synaptic information, subsequent phosphorylation by CaMKII of a particular substrate may encode memory, e.g. as ordered arrays of 6 bits (one ‘byte’).”
Quote in the paperSubstantial claim- Rests on an assumption: CaMKII activation represents synaptic information.
- Interpretationreasoning
Sets of 6 CaMKII kinase domains interacting with 6 tubulin dimers can provide 6 binary bits (64 possible states), comprising one byte.
“Sets of 6 CaMKII kinase domains interacting with 6 tubulin dimers can then provide 6 binary bits (64 possible states), comprising one byte.”
Quote in the paperSubstantial claim- Rests on an assumption: Each CaMKII kinase domain can phosphorylate a substrate or not, conveying 1 bit of information.
- Rests on an assumption: Each kinase domain can phosphorylate one tubulin dimer, either its α-monomer or its β-monomer equivalently.
- Interpretationcitation
Such patterns operate at multiple time scales to regulate biological systems.
“Microtubules can generate three-dimensional reaction-diffusion patterns [70], and we suggest such patterns operate at multiple time scales to regulate biological systems.”
Quote in the paperNot a substantial claim - Interpretationreasoning
In a B lattice with 9 tubulin dimers in a patch, sets of 6 CaMKII kinase domains can choose and phosphorylate α-, β-, or neither tubulin monomer in any 6 of 8 available dimers, yielding 5,281 possible information states per neighborhood patch of 9 tubulin dimers.
“With the central ‘address’ dimer unavailable for phosphorylation, sets of 6 CaMKII kinase domains can choose and phosphorylate α- (0), β- (1), or neither (2) tubulin monomer in any 6 of 8 available dimers.”
- Also stated in: § Summary · plain
“This yields 5,281 possible information states per neighborhood patch of 9 tubulin dimers.”
Quote in the paperSubstantial claim- Rests on an assumption: Each kinase domain can phosphorylate one tubulin dimer, either its α-monomer or its β-monomer equivalently.
- Also stated in: § Summary · plain
- Interpretationown data
CaMKII-tubulin phosphorylation encoding is robust against degradation.
“This indicates encoding which is robust against degradation, yet inexpensive, requiring on the order of 2% of overall brain metabolism for maximal encoding in all 1011 neurons.”
Quote in the paperSubstantial claim - Interpretationreasoning
On an A lattice, considering each tubulin dimer phosphorylated on one monomer or neither results in 6 ternary states (trits) or 729 possible encoding states per tryte.
“On an A lattice we also consider each tubulin dimer being phosphorylated either on its α-tubulin monomer (0), α-tubulin monomer (1), or neither (2), resulting in 6 ternary states (‘trits’) or 729 possible encoding states (per ‘tryte’).”
Quote in the paperSubstantial claim- Rests on an assumption: Each kinase domain can phosphorylate one tubulin dimer, either its α-monomer or its β-monomer equivalently.
- Interpretationreasoning
Interference patterns of periodic, coherent reaction-diffusion waves in cytoplasm and larger spatial scales could account for scale-free information patterns regulating biological systems including the brain.
“Interference patterns of periodic, coherent reaction-diffusion waves in cytoplasm and larger spatial scales could account for scale-free information patterns regulating biological systems including the brain.”
Quote in the paperNot a substantial claim - Interpretationreasoning
Because of cylindrical MT lattice geometry, such patterns reverberate, interfere and change nonlinearly.
“Because of cylindrical MT lattice geometry, such patterns reverberate, interfere and change nonlinearly.”
Quote in the paperSubstantial claim - Interpretationreasoning
Microtubule automata are in principle capable of information processing.
“Thus microtubule automata are in principle capable of information processing.”
Quote in the paperSubstantial claim - Premisecitation
Microtubules can generate three-dimensional reaction-diffusion patterns.
“Microtubules can generate three-dimensional reaction-diffusion patterns [70]”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [70] D Van De Ville, 2010, EEG microstate sequences in healthy humans at rest reveal scale-free dynamics., Proc Natl Acad Sci U S A source
Not checked in the free run.
- Interpretationreasoning
A feasible and robust mechanism exists for encoding synaptic information into structural and energetic changes of microtubule lattices by calcium-activated CaMKII phosphorylation.
“We demonstrate a feasible and robust mechanism for encoding synaptic information into structural and energetic changes of microtubule (MT) lattices by calcium-activated CaMKII phosphorylation.”
Quote in the paperSubstantial claim- The authors state this as an assumption: Input information may be encoded and processed in hexagonal microtubule lattices.
- Interpretationreasoning
CaMKII-tubulin phosphorylation encoding is inexpensive, requiring on the order of 2% of overall brain metabolism for maximal encoding in all 10^11 neurons.
“This indicates encoding which is robust against degradation, yet inexpensive, requiring on the order of 2% of overall brain metabolism for maximal encoding in all 1011 neurons.”
Quote in the paperNot a substantial claim - Interpretationreasoning
Potential information capacity for CaMKII encoding of hexagonal MT lattices is enormous.
“Consequently, potential information capacity for CaMKII encoding of hexagonal MT lattices is enormous.”
Quote in the paperSubstantial claim- Rests on an assumption: There are approximately 10^19 tubulins in the brain.
- Classified as probably not a substantial claim. 14
- May combine two claims. 12
Classified as probably not a substantial claim.
Findingown dataFigures 9 and 10 demonstrate an AND gate and an XOR gate in which MAPs convey inputs, with output along tubulin pathways.
“Figures 9 and 10 demonstrate two types of Boolean logic gates, an AND gate and an exclusive OR gate (XOR) in which MAPs convey inputs, with output along tubulin pathways.”
Quote in the paperSubstantial claimMay combine two claims.
FindingreasoningElectrostatic attraction for each kinase-monomer interaction is 10 kT (6 kcal/mol) lower bound, reaching a maximum bound of 60 kT (36 kcal/mol) when all 6 kinase regions are involved.
“Considering the positive potential region of an individual kinase domain to be 1 kT/e and the negative surface of an individual tubulin monomer to be −10 e gives an electrostatic attraction of 10 kT, or 6 kcal/mol at 310 K, for each kinase-monomer interaction, the lower bound of binding. This attraction reaches a maximum bound of 60 kT (36 kcal/mol) when all 6 kinase regions are involved.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
Findingnone givenFigures 11 and 12 show AND and XOR gates in which MAPs convey output of inputs and processes in tubulins within the MT.
“Figures 11 and 12 show AND and XOR gates in which MAPs convey output of inputs and processes in tubulins within the MT.”
Quote in the paperSubstantial claimMay combine two claims.
FindingreasoningThere are 2^6 possible encoding states for a single CaMKII-MT interaction resulting in the storage of 64 bits of information.
“Thus, there are 26 possible encoding states for a single CaMKII-MT interaction resulting in the storage of 64 bits of information.”
Quote in the paperSubstantial claim- The authors state this as an assumption: Each extended kinase can either phosphorylate at the S-T site on a tubulin substrate, or not.
May combine two claims.
Findingown dataComplementary electrostatics and mutual attraction exist between individual CaMKII kinase domains and tubulin surfaces.
“We show, first, complementary electrostatics and mutual attraction between individual CaMKII kinase domains and tubulin surfaces.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningSignaling and encoding in MTs and other cytoskeletal structures offer rapid, robust solid-state information processing which may reflect a general code for MT-based memory and information processing within neurons and other eukaryotic cells.
“Signaling and encoding in MTs and other cytoskeletal structures offer rapid, robust solid-state information processing which may reflect a general code for MT-based memory and information processing within neurons and other eukaryotic cells.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable), S4 (based).
InterpretationreasoningSignals propagating through MT-MAP logic circuits may extend throughout cytoskeletal networks, regulating synaptic function, cognition and behavior.
“Signals propagating through MT-MAP logic circuits may extend throughout cytoskeletal networks, regulating synaptic function, cognition and behavior.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningSynaptic information is conveyed as ordered arrays of six bits, and thus bytes, with 64 to 5,281 possible bit states per CaMKII-MT byte.
“conveying synaptic information as ordered arrays of six “bits”, and thus “bytes”, with 64 to 5,281 possible bit states per CaMKII-MT byte.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningInformation pertinent to memory must be stored elsewhere than transient synaptic membrane components, yet remain able to regulate synaptic plasticity.
“Therefore, information pertinent to memory must be stored elsewhere, yet remain able to regulate synaptic plasticity.”
Quote in the paperSubstantial claim- Rests on an assumption: Synaptic membrane components are transient, whereas memories can endure.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSimple rule-based interactions among neighbor cell states updating at discrete time steps can lead to complex patterns, computation and self-organization in cellular automata.
“Simple rule-based interactions among neighbor cell states updating at discrete time steps can lead to complex patterns, computation and self-organization in cellular automata.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [59] J Von Neumann, 1951, The general and logical theory of automata.
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationCaMKII is a dodecameric holoenzyme containing two hexagonal sets of six kinase domains.
“CaMKII has 12 kinase domains (6 on one side, 6 on the other), normally folded tightly in an inactive state to an association domain.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [10] A Hudmon, 2002, Structure–function of the multifunctional Ca<sup>2+</sup>/calmodulin-dependent protein kinase II., Biochem J source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationReaction-diffusion systems include periodic waves and hexagonal patterns, which oscillate, undergo phase transitions and are capable of information processing.
“Reaction-diffusion systems include periodic waves and hexagonal patterns, which oscillate, undergo phase transitions and are capable of information processing [41].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [41] V Castets, 1990, Experimental evidence of sustained standing Turing-type nonequilibrium chemical pattern., Phys Rev Lett source
Not checked in the free run.
Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).
InterpretationreasoningThe hexagonal bytes and trytes suggested here may reflect a real-time biomolecular information code akin to the genetic code.
“As MTs and CaMKII are widely distributed in eukaryotic cells, the hexagonal bytes and trytes suggested here may reflect a real-time biomolecular information code akin to the genetic code.”
Quote in the paperNot a substantial claim- Rests on an assumption: MTs and CaMKII are widely distributed in eukaryotic cells.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationIn proposed microtubule automata, tubulin states interact and update coherently at discrete time steps attributed to theorized or experimentally observed coherent MT resonances, potentially resulting in millions of synchronized updates per second.
“In such proposed microtubule automata, tubulin states interact and update coherently at discrete time steps attributed to theorized [62] or experimentally-observed coherent MT resonances, e.g. in the low megahertz range [53], potentially resulting in millions of synchronized updates per second [63].”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [62] H Fröhlich, 1968, Long-range coherence and energy storage in biological systems., International J Quant Chem source
Not checked in the free run.
- cites [53] S Sahu, 2012, Radio-frequency-induced ultrafast assembly of microtubules and their length-independent electronic properties., Nature Mater
Not checked in the free run.
- cites [63] R Penrose, 2011, Consciousness in the universe., J Cosmology
Not checked in the free run.
May combine two claims.
PremisecitationIn the brain, neuronal network structure, temporal dynamics, and representation of mental states are all scale-free, with self-similar patterns repeating at various temporal and spatial scales and locations.
“In the brain, evidence suggests neuronal network structure, temporal dynamics, and representation of mental states are all ‘scale-free’, with self-similar patterns repeating at various temporal and spatial scales and locations [68]–[71].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [68]–[71]
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationCortical neuron representation maps are organized hexagonally.
“Cortical neurons representation maps are organized hexagonally [65]”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [65] SB Paik, 2011, Retinal origin of orientation maps in visual cortex., Nature Neurosci source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationMTs have been modeled as von Neumann-type cellular/molecular automata in which tubulin subunits interact with neighbor tubulin states by rules based on dipole coupling strengths.
“For example MTs have been modeled as von Neumann-type cellular/molecular automata (‘microtubule automata’) in which tubulin subunits interact with neighbor tubulin states by rules based on dipole coupling strengths [50], [61].”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [50] S Rasmussen, 1990, Computational connectionism within neurons: A model of cytoskeletal automata subserving neural networks., Physica D source
Not checked in the free run.
- cites [61] S Smith, 1984, Cellular automata in cytoskeletal lattice proteins., Physica D source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationTuring patterns have been suggested in biological systems across scale, from intra-cellular processes to neuronal network organization.
“Turing patterns have been suggested in biological systems across scale, e.g. from intra-cellular processes [42] to neuronal network organization.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [42] DE Strier, 2007, Turing Patterns Inside Cells., PLoS ONE source
Not checked in the free run.
May combine two claims.
PremisecitationSimulations show oscillating wedge-shaped, triangular and hexagonal patterns of tubulin states, which evolve, compute and can learn.
“Simulations show oscillating wedge-shaped, triangular and hexagonal patterns of tubulin states, which evolve, compute and can learn [50].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [50] S Rasmussen, 1990, Computational connectionism within neurons: A model of cytoskeletal automata subserving neural networks., Physica D source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationGrid cells in entorhinal cortex record spatial location as apparent hexagonal maps, with different spatial scales at different layers of entorhinal cortex.
“‘grid cells’ in entorhinal cortex record spatial location as apparent hexagonal maps, with different spatial scales at different layers of entorhinal cortex [66], [67].”
Quote in the paperNot a substantial claim0 of 2 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationStable patterns of molecular concentrations could emerge through reaction, diffusion and inhibition.
“In 1953 Alan Turing [64] showed that stable patterns of molecular concentrations could emerge through reaction, diffusion and inhibition.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [64] AM Turing, 1953, The chemical basis of morphogenesis., Phil Trans R Soc B source
Not checked in the free run.
Probably not a substantial claim: may not pass S2 (checkable), S4 (based). May combine two claims.
InterpretationreasoningSuch encoded information engages in ongoing MT information processes supporting cognition and behavior, possibly by generating scale-free interference patterns via reaction-diffusion or other mechanisms.
“We suggest such encoded information engages in ongoing MT information processes supporting cognition and behavior, possibly by generating scale-free interference patterns via reaction-diffusion or other mechanisms.”
Quote in the paperNot a substantial claim
The paper relies on this without support.
Synaptic membrane components are transient, whereas memories can endure.
“synaptic receptors and channel proteins are transient, being synthesized and degraded in the protein lifecycle, and yet memories can last lifetimes.”
The authors state this as an assumption.
Each extended kinase can either phosphorylate at the S-T site on a tubulin substrate, or not.
“If each extended kinase can either phosphorylate at the S-T site on a tubulin substrate, or not, the process effectively conveys one bit of information”
The paper relies on this without support.
The combination of XOR and AND logic gates forms a universal set for computation.
“The combination of XOR and AND logic gates forms a universal set for computation in which all other logic gates (NOT, OR etc.) can be conceived.”
The paper relies on this without support.
CaMKII activation represents synaptic information.
“As CaMKII activation represents synaptic information, subsequent phosphorylation by CaMKII of a particular substrate may encode memory, e.g. as ordered arrays of 6 bits (one ‘byte’).”
The paper relies on this without support.
MTs and CaMKII are widely distributed in eukaryotic cells.
“As MTs and CaMKII are widely distributed in eukaryotic cells, the hexagonal bytes and trytes suggested here may reflect a real-time biomolecular information code akin to the genetic code.”
The paper relies on this without support.
Each CaMKII kinase domain can phosphorylate a substrate or not, conveying 1 bit of information.
“When activated by synaptic calcium influx, the snowflake-shaped CaMKII extends sets of 6 foot-like kinase domains outward, each domain able to phosphorylate a substrate or not (thus convey 1 bit of information).”
The paper relies on this without support.
Each kinase domain can phosphorylate one tubulin dimer, either its α-monomer or its β-monomer equivalently.
“Each kinase domain can phosphorylate one tubulin dimer, either its α- monomer or its β- monomer equivalently.”
The paper relies on this without support.
There are approximately 10^19 tubulins in the brain.
“There are approximately 1019 tubulins in the brain.”
The authors state this as an assumption.
Input information may be encoded and processed in hexagonal microtubule lattices.
“Assuming input information may be encoded and processed in hexagonal microtubule lattices, how could such information be expressed as output to regulate cytoplasmic and membrane activities?”
The paper relies on this without support.
How information is shared or encoded among biological levels in a common framework is largely unknown.
“How information is shared or encoded among these levels in a common framework is largely unknown.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Consistent with the Orch OR account, the cytoskeleton does play a major role in memory.
“Consistent with the Orch OR account, the cytoskeleton does play a major role in memory (Craddock et al. 2012).”
From A quantum microtubule substrate of consciousness is experimentally supported and solves the binding and epiphenomenalism problems (2025) · cites this paper as Craddock et al. 2012
The Introduction (page unavailable) says deficits in cytoskeletal function affect learning and memory and describes correlations between microtubule changes and memory. But the Discussion’s Conclusion (page unavailable) presents a proposed mechanism and suggests it may support cognition; it does not establish the stronger claim that the cytoskeleton plays a major role in memory. The reference to Orch OR is framing in the citing sentence, not a finding established by this source. (LLM, conf=0.85)
Experimental — accuracy not yet measuredSynaptic inputs can register information in dendritic-somatic MTs in brain neurons by metabotropic receptors, MAP2, and CaMKII, a hexagonal holoenzyme able to convey calcium ion influx to MT lattices by phosphorylation.
“Synaptic inputs can register information in dendritic-somatic MTs in brain neurons by metabotropic receptors, MAP2, and CaMKII, a hexagonal holoenzyme able to convey calcium ion influx to MT lattices by phosphorylation (Fig. 4 [64]).”
From Consciousness in the universe (2014) · cites this paper as [64]
The Introduction describes synaptic calcium influx activating CaMKII, and the Discussion’s Conclusion proposes that CaMKII phosphorylation can encode synaptic information in dendritic and somatic microtubule lattices. The Results describe CaMKII’s hexagonal structure, while the Introduction identifies MAP2 on dendritic microtubules. The paper refers to postsynaptic receptors but does not identify metabotropic receptors as the route in this proposed mechanism. (LLM, conf=0.86)
Experimental — accuracy not yet measuredDendritic-somatic MTs are capped by special MAPs that prevent de-polymerization, and are thus stable and suitable for long term information encoding and memory.
“Dendritic-somatic MTs are capped by special MAPs that prevent de-polymerization [63], and are thus stable and suitable for long term information encoding and memory (Fig. 4 [64]).”
From Consciousness in the universe (2014) · cites this paper as [64]
The Introduction (LTP, CaMKII and Microtubules; page unavailable) says dendritic and cell-body microtubules are capped and stabilized by specialized MAPs, and discusses information storage in microtubules. But it describes memory stored in microtubules as short-term and proposes further encoding in neurofilaments for long-term memory. It therefore does not fully support the cited clause’s implication that stable microtubules themselves provide long-term memory storage. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Six-bit pattern is described as storing 64 bits
MajorSix binary phosphorylation sites provide 64 possible states, but encode 6 bits, as the paper states elsewhere. The 64-bit claim confuses the number of states with the number of bits.
“Thus, there are 26 possible encoding states for a single CaMKII-MT interaction resulting in the storage of 64 bits of information.”
“Each set of six extended kinases on either side of a CaMKII holoenzyme can thus act collectively as 6 bits of information.”
Six-kinase binding energy is described as a per-event value
MinorThe results give 6 kcal/mol for each kinase-monomer interaction and 36 kcal/mol only when all six kinase regions are involved. The summary instead presents the full 6-36 kcal/mol range as applying per phosphorylation event.
“calculate binding energies in the range of 6 to 36 kcal/mol per CaMKII-tubulin phosphorylation event.”
“This attraction reaches a maximum bound of 60 kT (36 kcal/mol) when all 6 kinase regions are involved.”
Ternary-state summary assigns two states to α-tubulin
MinorThe summary assigns both phosphorylation states to the α-monomer, whereas the earlier definition assigns one to β-tubulin and the other to α-tubulin.
“On an A lattice we also consider each tubulin dimer being phosphorylated either on its α-tubulin monomer (0), α-tubulin monomer (1), or neither (2)”
“no phosphorylation (0), β-tubulin phosphorylation (1), or α-tubulin phosphorylation (2)”
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- Authors
- Craddock, T. J. A., Tuszynski, J. A., & Hameroff, S.
- Affiliations
- University of Alberta (CA)
- University of Arizona (US)
- Corresponding author
- Craddock, Travis J. A.
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-03-08
- Volume
- 8
- Issue
- 3
- Pages
- e1002421
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC3297561
- OpenAlex
- W2042941423
- Cited by
- 160
- References
- 97
- Citations by year
- 2026: 10 · 2025: 13 · 2024: 10 · 2023: 10 · 2022: 9 · 2021: 9 · 2020: 9 · 2019: 9 · 2018: 5 · 2017: 11 · 2016: 8 · 2015: 17 · 2014: 13 · 2013: 16 · 2012: 11
- FWCI
- 7.51
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PORTO@Iris (submittedVersion)
- NSUWorks (Nova Southeastern University) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Ministry of Advanced Education, Government of Alberta
- Alberta Cancer Foundation
- Allard Foundation
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Neuroscience › Cognitive Neuroscience › Memory and Neural Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
- Keywords
- CaMKII, microtubules, memory encoding, long-term potentiation, synaptic plasticity, phosphorylation, cytoskeletal signaling, molecular memory, calcium signaling
- MeSH terms
- Computer Simulation, Cytoskeleton, Humans, Memory, Models, Biological, Models, Chemical, Phosphorylation, Signal Transduction, Calcium-Calmodulin-Dependent Protein Kinase Type 2
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