1. Nutrigenomics
1. Health, Nutrition, DNA
2. History Biochemical Pathways, Vitamins and Omics
3. Triage Theory
4. Structural Proteins/DNA variations
5. Conclusions
David R. Bachinsky, Ph.D., M.S.
Cellanyx Diagnostics 5 June 2013

2. Genotypes and Nutrition ≠ simple Phenotypes

3. “The main distinguishing characteristic between man and the lower
animals is the desire to take pills.” Mark Twain

4. Nutrigenomics: goals and strategies. Michael Müller & Sander Kersten
http://www.nature.com/nrg/journal/v4/n4/full/nrg1047.html http://nutrigene.4t.com/
Nutrigenomics is a branch of nutritional genomics and is the study of the effects of foods
and food constituents on gene expression.
Nutritional genomics is a science studying the relationship between human genome,
nutrition and health
Michael Muller

5. Overweight and Obesity (CD) http://www.cdc.gov/obesity/data/adult.html
Obesity is common, serious and costly. More than one-third of U.S. adults (35.7%) are obese. The medical costs for people who are obese were
$1,429 higher than those of normal weight. Obesity affects some groups more than others. Non-Hispanic blacks have the highest age-adjusted rates
of obesity (49.5%) compared with Mexican Americans (40.4%), all Hispanics (39.1%) and non-Hispanic whites (34.3%).

6. Epigenetic Biomarkers May Predict If a Specific Diet and Exercise Regimen Will Work. 29 May
2013 . New research in The FASEB Journal describes five epigenetic biomarkers associated with better weight loss
response in Spanish adolescents participating in the 10-week EVASYON weight loss program. After validation, 5
regions located in or near AQP9, DUSP22, HIPK3, TNNT1, and TNNI3 genes showed differential methylation levels
between high and low responders to the multidisciplinary weight loss intervention. http://www.fasebj.org/content/27/6/2504
“Genotype Patterns Predict Weight Loss Success: The Right Diet Does Matter” INTERLEUKIN
GENETICS, INC. AND STANFORD UNIVERSITY REPORT GENETIC TEST IMPROVES WEIGHT LOSS SUCCESS AHA
Meeting. March 3, 2010. Individuals on genotype-appropriate diets lost 5.3 percent of body weight compared to
individuals on diets not matched to their genotype, who experienced only 2.3 percent weight loss. FABP2: Ala54Thr,
PPARG:Pro12Ala, ADRB2: Arg16Gly, Gln27Glu and ADRB3: Arg64Trp
http://scienceblogs.com/pharyngula/2008/07/22/epigenetics/
http://www.hgu.mrc.ac.uk/people/r.meehan_researchb.html

7. Randy Jirtle
http://randyjirtle.com/
Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene
Regulation. Robert A. Waterland and Randy L. Jirtle http://mcb.asm.org/content/23/15/5293.long
Virgin a/a females, 8 weeks of age, were assigned randomly to NIH-31 diet or NIH-31 supplemented with the methyl donors and cofactors folic acid,
vitamin B12, choline chloride, and anhydrous betaine
Maternal dietary methyl supplementation and coat color phenotype of Avy/a
offspring. Isogenic Avy/a animals representing the five coat color classes used to
classify phenotype. The Avy alleles of yellow mice are hypomethylated, allowing
maximal ectopic agouti expression. Avy hypermethylation silences ectopic agouti
expression in pseudoagouti animals, recapitulating the agouti phenotype.

8. Hungry Planet by Faith
D'Aluisio and Peter Menzel.
Shown is the weekly amount
of food consumed in different
countries.
http://www.books4yourkids.com/2012/12/what-
world-eats-by-faith-daluisio.html

9. 1. Health, Nutrition, DNA
2. History Biochemical Pathways, Vitamins and Omics
3. Triage Theory
4. Structural Proteins, DNA variations
5. Conclusions

10. James Lind, a British Royal Navy surgeon who, in 1747, identified that a quality in fruit
prevented the disease of scurvy in what was the first recorded controlled experiment.
The earliest documented case of scurvy was described by Hippocrates around 400
BC. The term vitamin was derived from "vitamine," a compound word coined in
1912 by the Polish biochemist Kazimierz Funk when working at the Lister Institute of
Preventive Medicine. The name is from vital and amine, meaning amine of life,
because it was suggested in 1912 that the organic micronutrient food factors that
prevent beriberi and perhaps other similar dietary-deficiency diseases might be
chemical amines. This proved incorrect for the micronutrient class, and the word
was shortened to vitamin.
Kazimierz Funk

11. A vitamin is an organic compound required by an
organism as a vital nutrient in limited amounts. An
organic chemical compound (or related set of
compounds) is called a vitamin when it cannot be
synthesized in sufficient quantities by an organism, and
must be obtained from the diet. http://en.wikipedia.org/wiki/Vitamin

12. The human disease network http://www.pnas.org/content/104/21/8685.abstract
(b) In the DGN, each node is a gene, with
two genes being connected if they are
implicated in the same disorder. The size
of each node is proportional to the
number of disorders in which the gene is
implicated (see key). Nodes are light gray
if the corresponding genes are associated
with more than one disorder class. Genes
associated with more than five disorders,
and those mentioned in the text, are
indicated with the gene symbol. Only
nodes with at least one link are shown.
In the HDN, each node corresponds to a
distinct disorder, colored based on the
disorder class to which it belongs, the name
of the 22 disorder classes being shown on
the right. A link between disorders in the
same disorder class is colored with the
corresponding dimmer color and links
connecting different disorder classes are
gray. The size of each node is proportional to
the number of genes participating in the
corresponding disorder

13. Flavor network and the principles of food pairing
Each node denotes an ingredient, the node color indicates
food category, and node size reflects the ingredient
prevalence in recipes. Two ingredients are connected if they
share a significant number of flavor compounds, link
thickness representing the number of shared compounds
between the two ingredients.
(A) The ingredients contained in two recipes (left column),
together with the flavor compounds that are known to be
present in the ingredients (right column). Each flavor
compound is linked to the ingredients that contain it, forming
a bipartite network. Some compounds (shown in boldface)
are shared by multiple ingredients. (B) If we project the
ingredient-compound bipartite network into the ingredient
space, we obtain the flavor network, whose nodes are
ingredients, linked if they share at least one flavor compound.
The thickness of links represents the number of flavor
compounds two ingredients share and the size of each circle
corresponds to the prevalence of the ingredients in recipes.
(C) The distribution of recipe size, capturing the number of
ingredients per recipe, across the five cuisines explored in our
study. (D) The frequency-rank plot of ingredients across the
five cuisines show an approximately invariant distribution
across cuisines.
Yong-Yeol Ahn,
Sebastian E. Ahnert,
James P. Bagrow
& Albert-László Barabási

14. Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes
http://www.sciencedirect.com/science/article/pii/S0092867412001663
Revolution in Personalized Medicine: First-Ever Integrative 'Omics' Profile Lets
Scientist Discover, Track His Diabetes Onset (March 2012)
http://www.sciencedaily.com/releases/2012/03/120315123020.htm
Geneticist Michael Snyder, PhD, has
almost no privacy. For more than
two years, he and his lab members
at the Stanford University School of
Medicine pored over his body's
most intimate secrets: the
sequence of his DNA, the RNA and
proteins produced by his cells, the
metabolites and signaling
molecules wafting through his
blood.
“A large database with the complete time-dynamic profiles for more individuals that acquire
infections and other types of diseases will be extremely valuable in the early diagnostics,
monitoring and treatment of diseased states.”

15. iPOP Goes the World: Integrated Personalized Omics Profiling and the Road
toward Improved Health Care http://www.cell.com/chemistry-biology/fulltext/S1074-5521%2813%2900174-
9#MainText integrated personal omic profiling (iPOP)
Highlights in iPOP
(A) Integration of DNA variants to assess disease risk
(RiskGraph, top panel) and a sample pharmacogenome
(bottom panel). Arrow heads point in the direction of
the change in posttest probability (%).
(B) Expression analysis (partial heatmap) of the
transriptome and proteome over a time course
spanning a respiratory syncytial viral (RSV) infection,
with glucose monitoring (bottom, onset of T2D). Genes
showing relative change in expression are clustered
and represented as a network of inter- and
intraconnected pathways: RNA (blue circle), protein
(yellow square), and both RNA and protein (green
hexagon). An example of a metabolite identified during
the time course is also shown (inset panel).
Schematic Representing the Implementation of iPOP for Personalized
Medicine
(A) Participant tissue sample (e.g., PBMC) is collected, while environment
(including diet, exercise, etc.), medical history, and clinical data are
recorded. T1 is the first time point.
(B) Selected omic analysis involved in a sample iPOP study (Chen et al.,
2012).
(C) Sample Circos plot (Krzywinski et al., 2009) of DNA (outer ring), RNA
(middle ring), and protein (inner ring) data matching to chromosomes.
(D) iPOP performed and integrated at multiple time points: T2, T3, T4 (viral
infected), and T5 up to Tn states, including disease state(s). Grey and green
forms represent a relatively healthy individual and a disease state,
respectively.
(E) Report data back to genetic counselor and medical practitioner with
better informed choices for prevention and/or treatment (matched with
pharmacogenetic data), if needed.

16. 1. Health, Nutrition, DNA
2. History Biochemical Pathways, Vitamins and Omics
3. Triage Theory
4. Structural Proteins, DNA variations
5. Conclusions

17. Bruce Ames
Dr. Ames is a Senior Scientist at Childrens Hospital Oakland Research Institute (CHORI), director of their Nutrition & Metabolism Center, and a Professor
Emeritus of Biochemistry and Molecular Biology, University of California, Berkeley.
He is a member of the National Academy of Sciences and he was on their Commission on Life Sciences. He was a member of the board of directors of the
National Cancer Institute, the National Cancer Advisory Board, from 1976 to 1982. He was the recipient of the General Motors Cancer Research
Foundation Prize (1983), the Tyler Environmental Prize (1985), the Gold Medal Award of the American Institute of Chemists (1991), the Glenn Foundation
Award of the Gerontological Society of America (1992), the Lovelace Institutes Award for Excellence in Environmental Health Research (1995), the Honda
Prize of the Honda Foundation, Japan (1996), the Japan Prize, (1997), the Kehoe Award, American College of Occup. and Environ. Med. (1997), the Medal
of the City of Paris (1998), the U.S. National Medal of Science (1998), The Linus Pauling Institute Prize for Health Research (2001), and the American
Society for Microbiology Lifetime Achievement Award (2001). His over 540 publications have resulted in his being among the few hundred most-cited
scientists (in all fields).

18. Triage Theory: Metabolism responds to moderate deficiency of an essential
vitamin or mineral so that the scarce cofactor is retained (by proteins) for
short term survival/reproduction while long term health/longevity proteins
associated with aging lose vitamins/minerals and are disabled. 40 essential
micronutrients (vitamins/minerals) and mild deficiencies associated with
aging (cancer, heart disease). Vitamin K and selenium, are well studied and
published examples. In addition, the Institute of Medicine sets the RDA
(Recommended Daily Allowance) two standard deviations above EAR
(Estimated Average Requirement), most of the US population is below EAR
for one or more vitamin/mineral. NHANES database indicates US
population: 56% below for magnesium, 12% zinc, 49% vitamin B6 (older
women), 16% iron (menstruating women). Low intakes of vitamin D,
calcium, potassium, omega-3 fatty acids, and vitamin K.

19. Deregulated Nutrient Sensing
The somatotrophic axis in mammals comprises the growth hormone (GH), which is
produced by the anterior pituitary, and its secondary mediator, insulin-like growth
factor 1 (IGF-1), produced in response to GH by many cell types, most notably
hepatocytes. The intracellular signaling pathway of IGF-1 is the same as that elicited by
insulin, which informs cells of the presence of glucose. For this reason, IGF-1 and
insulin signaling are known as the “insulin and IGF-1 signaling” (IIS) pathway.
Remarkably, the IIS pathway is the most conserved aging-controlling pathway in
evolution, and among its multiple targets are the FOXO family of transcription factors
and the mTOR complexes, which are also involved in aging and conserved through
evolution Genetic polymorphisms or mutations that reduce the functions of GH, IGF-1
receptor, insulin receptor, or downstream intracellular effectors such as AKT, mTOR,
and FOXO have been linked to longevity, both in humans and in model organisms,
further illustrating the major impact of trophic and bioenergetic pathways on
longevity.
Consistent with the relevance of deregulated nutrient sensing as a hallmark of aging,
dietary restriction (DR) increases lifespan or healthspan in all investigated eukaryote
species, including nonhuman primates
The Hallmarks of Aging. http://www.cell.com/abstract/S0092-8674%2813%2900645-4#MainText

20. 1. Health, Nutrition, DNA
2. History Biochemical Pathways, Vitamins and Omics
3. Triage Theory
4. Structural Proteins, DNA variations
5. Conclusions

21. A single-nucleotide polymorphism is a DNA sequence variation occurring when a single
nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between
members of a biological species or paired chromosomes in a human. For example, two
sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a
difference in a single nucleotide. In this case we say that there are two alleles. As of 26 June
2012, dbSNP listed 53,558,214 SNPs in humans http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
A SNP is a single-letter change in DNA, part of the natural
genetic variation within a population.
Image courtesy of Lauren Solomon, the Broad Institute

23. PMID 19103647] rs12934922 (R267S) and rs7501331 (A379V) double mutant have a reduced catalytic activity of beta-carotene by 57%. Female
volunteers carrying the T variant of rs7501331 (379V) had a 32% lower ability to convert Beta-carotene, and those carrying at least one T in both
SNPs show a 69% lower ability to convert Beta-carotene into retinyl esters.
rs7501331: the frequency of the wild-type C allele and variant T allele was 76 and 24%, respectively; 56% of the population was CC wild-type
genotype, and 39% was heterozygote CT with the TT variant present in 5% of the population.
rs12934922: the frequency of the wild-type A allele and variant T allele was 58 and 42%, respectively; 38% of the population was AA wild-type
genotype, 40% was heterozygote AT, and 22% was TT homozygote
[PMID 19557453] beta-Carotene conversion products and their effects on adipose tissue.
[PMID 19844255] Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-
Canadian subjects.
[PMID 21091228] Genetic variants in BCMO1 and CD36 are associated with plasma lutein concentrations and macular pigment optical density in
humans.
[PMID 22113863] Single nucleotide polymorphisms upstream from the beta-carotene 15,15'-monoxygenase gene influence provitamin A
conversion efficiency in female volunteers.
“Vitamins” search returns over 500 SNPs and counting

24. MTRR, Methionine Synthase Reductase, Ile22Met, reduction in enzyme activity, increases in
homocysteine.
MTR, Methionine Synthase, Asp919Gly, increased enzyme activity, reduction in homocysteine.
MTHFR, Methylenetetrahydrofolate reductase, Ala222Val, Glu429Ala, reduced enzyme activity,
increased homocysteine.
LPL, Lipoprotein Lipase, Ser474Stop, increased LPL levels.
LIPC, Hepatic Lipase, -293G>A (insulin stimulation blunted), -557C>T (diminished activity).
CEPT, Cholesterol Ester Transfer Protein, 279G>A, lower levels of CETP/lower LDL/VLDL levers.
GSTP1, Glutathione-S-Transferase, Ile105Val, Ala114Val, decreased enzyme activity.
GSTM1, GSTT1, Glutathione-S-Transferase, deletions.
CBS, Cystathionine Beta Synthase, 699C>T, increased enzyme activity, lower homocysteine
levels.
Cubulin Receptor (B12), Rs11254363.
LRP2 (Megalin/gp330), Rs2544390, serum uric acid (Japanese/alcohol)

25. This variation accounts for roughly 12% of human genomic DNA and each variation
may range from about one kilobase (1,000 nucleotide bases) to several megabases in
size. CNVs contrast with single-nucleotide polymorphisms (SNPs), which affect only
one single nucleotide base.
Copy-number variations (CNVs)—a form of structural variation—are alterations of the
DNA of a genome that results in the cell having an abnormal number of copies of one
or more sections of the DNA.
http://en.wikipedia.org/wiki/Copy-number_variation
Evan Eichler
http://www.gs.washington.edu/faculty/eichler
.htm
http://www.nature.com/nature/journal/v464/n7289/full/nature08516.html

26. Sequence alignment and domain organization of human thioredoxin reductases and homologus proteins. (A) The sequences of cytosolic (TrxR1; entry:
Q16881) and mitochondrial (TrxR2; entry: Q9NNW7) thioredoxin reductases and of thioredoxin glutathione reductase (TrxR3; entry: Q86VQ6) were obtained
from Swiss-Prot/TrEMBL protein sequence database and aligned with Clustal W 2.0.10 Multiple Sequence Alignment [197]. Selenocysteine (U) appears as
the penultimate amino acid. (B) Domain organization of human TrxR1 (hTrxR1), TrxR2 (hTrxR2), TrxR3 (hTrxR3), E. coli TrxR and human glutathione reductase
(hGR). The different domains are specified below each schematic representation, while in the upper part the motifs of the active centers are reported.
Thioredoxin reductase: A target for gold
compounds acting as potential anticancer
drugs.
http://www.sciencedirect.com/science/article/pii/S0010854509000770
Clustal is a widely used multiple sequence
alignment computer program. In
bioinformatics, Basic Local Alignment Search
Tool, or BLAST, is an algorithm for comparing
primary biological sequence information, such
as the amino-acid sequences of different
proteins or the nucleotides of DNA sequences.
A BLAST search enables a researcher to
compare a query sequence with a library or
database of sequences, and identify library
sequences that resemble the query sequence
above a certain threshold.

27. Genetic map of Europe; genes vary as a function of distance
http://blogs.discovermagazine.com/gnxp/2008/08/genetic-map-of-europe-genes-vary-as-a-
function-of-distance/#.UadHgZyGdsI
Razib Khan, Gene Expression Blog/Discover
Genetic Map of East Asia
http://scienceblogs.com/gnxp/2008/12/07/genetic-map-of-east-asia/
Genetic variation within Africa (and the world)
http://blogs.discovermagazine.com/gnxp/2010/08/genetic-variation-within-
africa-and-the-world/#.UaeP8JyGdsI

28. Differences in genetic risk among populations.
Each population is ranked by risk, which is denoted by a color. Populations with the greatest risk are bright red, and those with the lowest risk are green. (A)
Populations for East Asia and the Americas have lower genetic risk for type 2 diabetes than those from Africa and Europe. Genetic risk differentiation is sharply
divided along major population migration events. Type 2 diabetes is represented by 16 SNPs. (B) Genetic risk for biliary liver cirrhosis is represented by 44 SNPs.
Genetic risk peaks in East Asia and in the Karitiana population in South America. The background is a public domain world map from NASA Earth Observatory
(http://eoimages.gsfc.nasa.gov/images/im​agerecords/73000/73909/world.topo.bathy.​200412.3×5400×2700.jpg);an interactive online tool is available at
http://geneworld.stanford.edu using Google Maps technology.
doi:10.1371/journal.pgen.1003447.g001 Analysis of the Genetic Basis of Disease in the Context of Worldwide Human Relationships and Migration
Atul Butte
http://buttelab.stanford.edu/
Erik Corona, Rong Chen, Martin Sikora, Alexander A. Morgan,
Chirag J. Patel, Aditya Ramesh, Carlos D. Bustamante, Atul J.
Butte. (23 May 2013) Analysis of the Genetic Basis of Disease in
the Context of Worldwide Human Relationships and Migration.
PLoS Genetics, 2013; 9 (5): e1003447 DOI:
10.1371/journal.pgen.1003447

29. Sequence alignment with predicted secondary structure for vitamin D hydroxylases. Invariant
(black-shaded) and partially conserved (green-shaded) residues in mitochondrial (CYP24A1,
CYP27A1, CYP27B1) and microsomal (CYP2R1, rat CYP2J3, CYP2D6, CYP3A4) proteins are
associated with the heme-binding site (thiolate) and structural motifs such as the ERR triad (not
shown). Predicted secondary structures with helices (blue) and β-sheet structures (gold) are shown
above the sequence alignments. Missense mutations (red-shaded) associated with
cerebrotendinous xanthomatosis (CYP27A1 deficiency) and vitamin D dependency rickets type 1
(CYP27B1 deficiency) are described in Table 1. Sequences were retrieved from Entrez
(www.ncbi.nlm.nih.gov/Entrez/index.html) and the Cytochrome P450 Homepage
(drnelson.utmem.edu/CytochromeP450.html) and adjusted manually using GeneDoc v2.6 in a
larger alignment (not shown) of species homologs and crystal structures, including CYP2B4,
CYP2C5, CYP2C8, CYP2C9, CYP3A4, CYP51 (Mycobacterium tuberculosis), CYP119 (Sulfolobus
solfactaricus) and P450Bm-3, cam, eryF and terp
Different views of the homology model of
CYP24A1. The homology model of CYP24A1
is viewed down the putative substrate
access channel (a) and from above the distal
heme face (b). The tertiary structure of the
heme distal cavity is bordered by the β1
sheet (center, purple), β3a strand (yellow),
β5 hairpin (cyan), B′-helix (green), F-helix
(orange) and the loop (center, pink)
between the F-helix (orange) and the G-
helix (red). Parts of the A- and A′-helices
(gray) are positioned to contact a substrate
access channel. The C-helix (purple) is also
shown. Traces of other secondary structural
elements are also visible in the figure. The
model was constructed and energy-
minimized using SYBYL6.8.
Enzymes involved in the activation and inactivation of vitamin D
http://www.sciencedirect.com/science/article/pii/S0968000404002701

30. The Multifunctional Properties and Characteristics of Vitamin D-binding Protein
http://www.sciencedirect.com/science/article/pii/S1043276000003179
The vitamin D-binding protein gene (DBP) and the albumin family
members are linked on human chromosome 4. DBP is encoded by a
single gene on human chromosome 4, sublocalized to bands 4q11–q13,
and linked to its three other family members (4q11–q22). Recently, this
region has been mapped, and this family of genes was found to be
linked as shown, with ≈1.5 megabase pairs separating DBP from the ALB
gene5. Arrows indicate directions of transcription. Abbreviations: AFM,
gene encoding α-albumin/atamin; AFP, gene encoding α-fetoprotein;
ALB, gene encoding albumin.
Amino acid sequence and predicted secondary structure features of human
vitamin D-binding protein (DBP) (GC*1S allele). The 458 amino acids of DBP
are shown folded into their disulfide-bonded, triple domain structure
(indicated on the left). The third domain is truncated in DBP but is full-length
in albumin (ALB) and α-fetoprotein (AFP). The smaller circles mark the
positions of residues present in ALB and AFP but absent in DBP (Ref. 8). A
disulfide bond that forms a loop containing the sterol-binding region (green;
residues 35–49), not present in either ALB or AFP, is indicated by the orange
line linking residues 13 and 59. All 28 cysteine residues are conserved in all
known DBP sequences. The experimentally determined actin-binding
domain (yellow; residues 373–403) is also indicated15. A multiple alignment
of the six known DBP amino acid sequences was made; namely, human8,
rabbit11, rat9, mouse10, turtle12 and chicken13. Only those residues
showing identity or conservative substitutions in all six species are shaded
(red or pink, respectively). Thus, the figure demonstrates the very high level
of homology among DBP sequences from reptiles to human.

32. Vitamin D-binding protein also known as gc-globulin (group-specific
component) is a protein that in humans is encoded by the GC gene.
http://en.wikipedia.org/wiki/Vitamin_D-binding_protein
Retinol-binding proteins (RBP) are a family of proteins with diverse
functions. They are carrier proteins that bind retinol. Assessment of
retinol-binding protein is used to determine visceral protein mass in
health-related nutritional studies.
http://en.wikipedia.org/wiki/Retinol_binding_protein
Cubilin (CUBN) acts as a receptor for intrinsic factor-vitamin
B12 complexes. The role of receptor is supported by the
presence of 27 CUB domains. Cubulin is located within the
epithelium of intestine and kidney. Mutations in CUBN may
play a role in autosomal recessive megaloblastic anemia

33. Top: schematic drawing of amino acids contributing to substrate binding in DATAs, BCATs and ADCLs. The external aldimines, which are formed after binding and
transimination of the respective substrates with the PLP cofactor of the enzymes, are shown. Blue amino acids are part of binding pocket A and amino acids of
binding pocket B are shown in green. The gray shaded circle represents the glycine or valine, depending on the transaminase, that is located behind the carboxyl
group. The red threonine residue is important in the catalytic mechanism for shuttling of a proton during the reaction transition state. Bottom: sequence motifs
derived from multiple-sequence alignments are given using the same color code, showing that amino acids important for substrate binding in the active site are
rather conserved and can be used for a prediction of the substrate specificity of PLP-dependent fold class IV enzymes as well as for the enantiopreference of the
transaminases within this fold class
Rational assignment of key motifs for function guides in silico enzyme identification
http://www.nature.com/nchembio/journal/v6/n11/full/nchembio.447.html
Identification of key amino acid motifs that allow prediction of function of PLP-dependent
fold class IV proteins.

34. How a protein binds b12: a 3.o angstrom x-ray structure of the b12-
binding domains of methionine synthase
The core structure of the cobalamin-binding domain is characterised
by a five-stranded alpha/beta (Rossmann) fold, which consists of 5
parallel beta-sheets surrounded by 4-5 alpha helices in three layers
(alpha/beta/alpha). Upon binding cobalamin, important elements of
the binding site appear to become structured, including an alpha-
helix that forms on one side of the cleft accommodating the
nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can
be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-
on) according to the pH. When bound to the cobalamin-binding
domain, the dimethylbenzimidazole ligand is replaced by the active
histidine (His-on) of the DXHXXG motif. The replacement of
dimethylbenzimidazole by histidine allows switching between the
catalytic and activation cycles. In methionine synthase the
cobalamin cofactor is sandwiched between the cobalamin-binding
domain and an approximately 90 residues N-terminal domain
forming a helical bundle comprising two pairs of antiparallel helices.
This N-terminal domain forms a 4-helical bundle cap, in the
conversion to the active conformation of this enzyme, the 4-helical
cap rotates to allow the cobalamin cofactor to bind the activation
domain.
B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This
histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif
of the domain

35. Quinone Oxidoreductases and Vitamin K Metabolism
http://www.sciencedirect.com/science/article/pii/S0083672907000052

36. Genotype-phenotype association studies in clinically well characterized patients with
inherited bleeding disorders. Prof. Dr. Johannes Oldenburg http://www.herz-kreislauf-
netz.de/index.php?id=58&L=1&BF=1

38. Vitamin Analogs used in cancer (Folate) and blood thinning treatments (vitamin K)
"We estimate that formally integrating genetic testing into routine warfarin therapy
could allow American warfarin users to avoid 85,000 serious bleeding events and 17,000
strokes annually. We estimate the reduced health care spending from integrating genetic
testing into warfarin therapy to be $1.1 billion annually, with a range of about $100
million to $2 billion.“ http://www.clotcare.com/warfaringenetictesting.aspx

39. http://snpedia.com/index.php/Rs1800566
rs1800566 (C609T, Pro187Ser) is a snp within NQO1 (NAD(P)H dehydrogenase
(quinone 1)). A Ser (T) at this location denotes the NQO1*2 allele.
NAD(P)H:quinone oxidoreductase 1 NQO1*2 genotype (P187S) is a
strong prognostic and predictive factor in breast cancer
http://www.nature.com/ng/journal/v40/n7/full/ng.155.html
Coenzyme Q10 supplementation reduces HF admissions and improves survival: Q-
SYMBIO
"CoQ10 should be considered as a part of the maintenance therapy of patients with
chronic heart failure.“ 31 May 2013

40. Conclusions
1. DNA and nutrients impact health in a diversity of ways
2. Triage theory distinguishes short term and long term needs
3. Vitamin/Mineral binding domains conserved
4. Variations in binding domains lead to differences in requirements
5. Multiple proteins impact health including transporters, enzymes

42. The rs11144870 SNP in the riboflavin kinase (RFK) gene on chromosome 9 was associated with 8-week treatment response (odds ratio
(OR)=0.42, P=1.04 × 10−6).
Pharmacogenomics of selective serotonin reuptake inhibitor treatment for major depressive disorder: genome-wide associations and functional genomics
In enzymology, a riboflavin kinase (EC 2.7.1.26) is an enzyme that catalyzes the chemical reaction
ATP + riboflavin --- ADP + FMN
Thus, the two substrates of this enzyme are ATP and riboflavin, whereas its two products are ADP and FMN.
Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (EC 2.7.1.26), which converts it into FMN, and FAD
synthetase (EC 2.7.7.2), which adenylates FMN to FAD

43. In molecular biology, the Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that
binds medium- and long-chain acyl-CoA esters with very high affinity and may function as
an intracellular carrier of acyl-CoA esters. ACBP is also known as diazepam binding inhibitor
(DBI) or endozepine (EP) because of its ability to displace diazepam from the
benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore
possible that this protein also acts as a neuropeptide to modulate the action of the GABA
receptor
Acyl-CoA binding protein: “Brain Makes
Its Own Version of Valium
http://www.sciencedaily.com/releases/2013/05/130530132429.htm
Rs8192506
acyl-CoA-binding protein (ACBP) single nucleotide polymorphisms
Rs2084202
Association of acyl-CoA-binding protein (ACBP)

44. Tocopherol Activity Correlates with Its Location in a Membrane: A New
Perspective on the Antioxidant Vitamin E
http://pubs.acs.org/doi/abs/10.1021/ja312665r?ref=tw

45. Vitamin B12 transporter
http://en.wikipedia.org/wiki/ATP-binding_cassette_transporter
Intrinsic factor (IF) also known as gastric intrinsic factor (GIF) is a glycoprotein
produced by the parietal cells of the stomach. It is necessary for the
absorption of vitamin B12 later on in the small intestine. In humans, the
gastric intrinsic factor protein is encoded by the GIF gene.
(1) Dietary vitamin B12 is normally bound to proteins in food and is provided by food products
of animal origin.
(2) Pepsin and acid pH in the stomach will degrade these food proteins and release vitamin
B12.
(3) The vitamin B12 that is now free then binds to one of the three vitamin B12 binding
proteins, called haptocorrin, which is produced by the salivary glands and the parietal cells in
the stomach. In the duodenum the pH is now less acidic and this allows pancreatic proteases
to degrade the haptocorrin, and vitamin B12 (both newly ingested and from the bile duct) is
released again and binds tightly to Intrinsic Factor produced by parietal cells.
(4) In the mucosal cells of the distal ileum the vitamin B12-Intrinsic Factor complex is
recognised by special receptors.
(5) Vitamin B12 then enters the blood bound to another binding protein, transcobalamin, the
complex is known as holotranscobalamin (Active B12). The majority of vitamin B12 (70-80%) in
blood is bound to haptocorrin and only a minor proportion (20-30%) is bound to
transcobalamin.
(6) Holotranscobalamin (Active B12) is the biologically active fraction of vitamin B12 in the
blood as it is in only this form that vitamin B12 is delivered to all the cells of the body.
(7) Vitamin B12 absorbed in the intestine subsequently gets transported to the liver via the
portal system.
(8) There is extensive enterohepatic circulation of vitamin B12 and B12 is transported from the
liver, via the bile duct, to the duodenum

46. Table 1. Ligand specificity of LDLR family membersa
Ligands Physiological category LDLR family membersb and c
RAP Chaperone A,B,C,D,E,H (+)
HSP-96 Chaperone B (+)
Apolipoprotein E LM, AD A,B,C,D,E,F,J (+)
Apolipoprotein B LM A,C (+)
β2-Glycoprotein C (+)
Apolipoprotein J/clusterin/Sp40,40 LM C,D (+); B (−)
Apolipoprotein J-amyloid β AD C (+)
Lipoprotein (a) LM A,B,C,D (+)
Lipoprotein lipase LM A,B,C,D,F (+)
Hepatic lipase LM B (+)
Vitellogenin LM G (+)
Cubilin LM, VM C (+)
α2-Macroglobulin-protease complexes PH B,F (+); C (−)
Pro-uPA PH B,C,D (+)
UPA-PAI-1 PH B,C,D (+)
UPA-protease nexin-1 PH B,D (+)
TPA PH B,H (+)
TPA-PAI-1 PH B,C (+)
Thrombin-PAI-1 PH B (+)
Thrombin-protease nexin 1 PH B (+)
Thrombin-antithrombin III PH B (+)
Thrombin-heparin cofactor II PH B (+)
Trypsin-a1-antitrypsin PH B (+)
Coagulation factor VIII PH B (+)
Coagulation factor Ixa PH B (+)
Coagulation factor Xa-TFPI PH B (+)
TFPI PH B,D (+)
Aprotinin PH C (+)
Cathepsin G-α1 antichymotrypsin PH C (+); B (−)
Elastase-α1 antitrypsin PH B,C (+)
MMP-13 PH B (+)
MMP-9 PH B (+)
Thrombospondin-1 AG B,C,D (+)
Thrombospondin-2 AG B (+)
Thrombospondin-2/MMP2 PH, AG B (+)
Reelin ND D,F (+)
Alzheimer's precursor protein PH B (+)
Transcobalamin-vitamin B12 VM C (+)
Vitamin D-binding protein VM C (+)
Retinol-binding protein VM C (+)
Thyroglobulin HM C (+)
Parathyroid hormone HM C (+)
Insulin HM C (+)
Prolactin HM C (+)
And more……
Diverse roles for the LDL receptor
family
http://www.sciencedirect.com/science/article/pii/S1043276001005264
Dudley K. Strickland W. Scott Argraves

48. The Nutrition Source
http://www.hsph.harvard.edu/nutritionsource/
http://www.hsph.harvard.edu/walter-willett/
Walter Willett, Fredrick John Stare
Professor of Epidemiology and Nutrition
Chair, Department of Nutrition, Harvard
School of Public Health

49. In the patients, a characteristic urinary protein profile with increased urinary excretion of
vitamin D-binding protein, retinol-binding protein and albumin was associated with
absence of, or reduced, proximal tubular endocytic uptake as shown by renal
immunohistochemistry.
Renal phenotypic investigations of megalin-deficient patients’: novel insights into
tubular proteinuria and albumin filtration.
http://ndt.oxfordjournals.org/content/early/2012/10/08/ndt.gfs462.abstract

51. Concentration-function relations for vitamin C. The solid line represents schematically the amount of vitamin C that will prevent scurvy with a
margin of safety, on the basis of guidelines described in the text. The dashed line represents another putative function of vitamin C
independent of preventing scurvy. The dotted line represents a putative genetic variation that has reduced maximal function. B: Relation
between vitamin C dose and steady state plasma concentration. The relation between vitamin C dose and plasma concentration for men is
shown by the solid line (data derived from reference 5-Food and Nutrition Board, Panel on Dietary Antioxidants and Related Compounds.
Vitamin C: Dietary Reference Intakes for vitamin C, vitamin E, selenium, and carotenoids. Washington, DC: National Academy Press, 200095–
185). The dashed line represents a shift in achieved concentration as a consequence of a putative polymorphism in vitamin C metabolism or
transport. “Vitamin C: working on the x-axis” (AJCN 2009) http://ajcn.nutrition.org/content/90/5/1121.full

52. The Thiamine diphosphate dependent Enzyme Engineering Database: A tool for the systematic
analysis of sequence and structure relations http://www.biomedcentral.com/1471-2091/11/9

54. In molecular biology, the vitamin B12-binding domain is a protein domain which binds to cobalamin (vitamin B12). It can bind two different forms of the
cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains
are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes
that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the
cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-
binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary
sequence motif of the domain. Proteins containing the cobalamin-binding domain include:
nmr structure of glutamate
mutase (b12-binding subunit)
complexed with the vitamin
b12 nucleotide

56. LDL Receptor Gene Family. Modular Domain Assembly and Pleiotropy. Pleiotropy
occurs when one gene influences multiple phenotypic traits.

57. Differences among individuals for most quantitative or complex traits such as reading ability are
distributed as a normal bell-shaped curve. Multiple genes influence complex traits as probabilistic
propensities rather than predetermined programmes. Here the different genetic make-up of
individuals with respect to two hypothetical genes involved in reading ability is shown for 100
individuals (each person is represented by an oval), with five of these individuals (those on the
extreme left) receiving a diagnosis of reading disability. The green ovals indicate that the individual
has the disabling variant of one gene and blue ovals denote the disabling variant of the other gene.
Neither gene is necessary or sufficient for low scores, even for individuals who have disabling
variants of both genes (red ovals). This QTL perspective suggests that genes associated with
common disorders such as reading disability may represent the quantitative extreme of the same
genes that are responsible for variation throughout the population.
http://www.nature.com/nature/journal/v402/n6761supp/full/402c25a0.html

58. Genes encoding for isocitrate dehydrogenases 1 and 2, IDH1 and IDH2, are frequently
mutated in multiple types of human cancer. Mutations targeting IDH1 and IDH2 result in
simultaneous loss of their normal catalytic activity, the production of α-ketoglutarate (α-
KG), and gain of a new function, the production of 2-hydroxyglutarate (2-HG). 2-HG is
structurally similar to α-KG, and acts as an α-KG antagonist to competitively inhibit
multiple α-KG-dependent dioxygenases, including both lysine histone demethylases and
the ten-eleven translocation family of DNA hydroxylases. Abnormal histone and DNA
methylation are emerging as a common feature of tumors with IDH1 and IDH2 mutations
and may cause altered stem cell differentiation and eventual tumorigenesis.
Therapeutically, unique features of IDH1 and IDH2 mutations make them good
biomarkers and potential drug targets.