Genome-Wide Investigation of Exogenous Female Hormones, Genetic Variation, and Venous Thromboembolism Risk.

BACKGROUND: Increased risk of venous thromboembolism (VTE) is a life-threatening side effect for users of oral contraceptives (OCs) or hormone therapy (HT). OBJECTIVES: To investigate the potential for genetic predisposition to VTE in OC or HT users, we conducted a gene-by-environment (GxE) case-only meta-analysis of genome-wide association studies (GWAS). METHODS: Use or non-use of OCs (7 studies) or HT (8 studies) at the time of the VTE event was determined by pharmacy records or self-report. A synergy index (SI) was modeled for each variant in each study and estimated supra-multiplicative GxE interaction. The SI parameters were first meta-analyzed across OC and HT studies, and subsequently meta-analyzed to obtain an overall estimate. The primary analysis was agnostic GWAS and interrogated all imputed genotypes using a p-value threshold of <5.0x10-8; secondary analyses were candidate-based. RESULTS: The VTE case-only OC meta-analysis included 2,895 OC users and 6,607 non-users; the case-only HT meta-analysis included 2,434 HT users and 12,793 non-users. In primary GWAS meta-analyses, no variant reached genome-wide significance, but the smallest p-value approached statistical significance: rs9386463 (p = 5.03x10-8). We tested associations for 138 candidate variants and identified 2 that exceeded statistical significance (0.05/138=3.62x10-4): F5 rs6025 (p = 1.87x10-5, SI = 1.29: previously observed) and F11 rs2036914 (p = 2.0x10-4, SI = 0.91; new observation). CONCLUSIONS: The candidate-variant approach to identify supra-multiplicative associations between genetic variation and OC-HT use identified a new association with common genetic variation in F11 while the agnostic interrogations did not yield new discoveries.

Sex-specific genetic risks for adverse outcomes after coronary revascularization procedures.

Men and women have differing risks of adverse events after revascularization procedures and these differences could be partially driven by genetics. We studied the sex-specific differences in associations of polygenic risk scores (PRSs) with atrial fibrillation (AF), ischaemic stroke (STR), intracranial haemorrhage (ICH), myocardial infarction (MI) and gastrointestinal haemorrhage (GIH) in coronary revascularization patients. The study cohort comprised 5561 and 17 578 revascularized women and men. All participants underwent genotyping and register-based follow-up from 1961 to 2021. We calculated PRSs for all individuals and used Cox models with interaction term to examine the sex-specific associations between the PRSs and adverse outcomes after revascularization. The AF-PRS was more strongly associated with AF in men [hazard ratio (HR) per 1 standard deviation increase, 1.16; 95% confidence interval (CI), 1.12-1.19; P = 7.6 × 10-22) than in women (P for interaction 0.006). Conversely, ICH-PRS was more strongly associated with ICH after revascularization in women (HR, 1.32; 95% CI, 1.08-1.62; P = 0.008) than in men (P for interaction 0.008). We observed no sex-specific differences for the associations of PRSs with STR, MI or GIH. The genetic risk of AF after revascularization is greater in men than in women, and vice versa for ICH. Sex-specific PRSs could be used to identify individuals in high genetic risk for these complications.

Increased risk of dementia differs across cardiovascular diseases and types of dementia - Data from a nationwide study.

AIMS: Dementia is a major health problem. Cardiovascular diseases (CVD) and risk factors are associated with incident dementia. However, whether there is an association among CVD, Alzheimer's disease (AD) and vascular dementia (VD) at the population level remains unclear. METHODS: We analysed the association between CVD (heart failure [HF], atrial fibrillation [AF], myocardial infarction [MI], peripheral arterial disease, stroke and transient ischemic attack) and the incidence of dementia using nationwide FinnGen data of 218,192 individuals. The last follow-up information on dementia was available from October 2021. RESULTS: The age at the end of the follow-up was 61.7 ± 17.1 years, and 53% were women. Overall, we observed 9701 (4.4%) dementia, 6323 (2.9%) AD and 1918 (0.7%) VD cases. Individuals with CVD had a higher risk of developing dementia than unexposed individuals. In the multivariable-adjusted Cox models, stroke was most strongly associated with dementia (hazard ratio [HR] 1.7, 95% confidence interval [CI] 1.6-1.8). CVD was more strongly associated with VD than with AD. Individuals with HF and MI had an increased risk of AD (HF: HR 1.11, 95% CI 1.04-1.19; MI: HR 1.10, 95% CI 1.02-1.18). AF was associated with VD (HR 1.58, 95% CI 1.42-1.77), but not with AD (HR 1.03, 95% CI 0.97-1.09). Clinical characteristics, such as diabetes, smoking and alcohol abuse, were associated with both types of dementia. CONCLUSION: All major CVDs were associated with an increased risk of developing dementia, particularly VD. Therefore, CVD onset should prompt an assessment of cognitive decline and possible preventive measures.

Risk of Midlife Stroke After Adverse Pregnancy Outcomes: The FinnGen Study.

BACKGROUND: Adverse pregnancy outcomes (APO) contribute to higher risk of maternal cerebrovascular disease, but longitudinal data that include APO and stroke timing are lacking. We hypothesized that APO are associated with younger age at first stroke, with a stronger relationship in those with >1 pregnancy with APO. METHODS: We analyzed longitudinal Finnish nationwide health registry data from the FinnGen Study. We included women who gave birth after 1969 when the hospital discharge registry was established. We defined APO as a pregnancy affected by gestational hypertension, preeclampsia, eclampsia, preterm birth, small for gestational age infant, or placental abruption. We defined stroke as first hospital admission for ischemic stroke or nontraumatic intracerebral or subarachnoid hemorrhage, excluding stroke during pregnancy or within 1 year postpartum. We used Kaplan-Meier survival curves and multivariable-adjusted Cox and generalized linear models to assess the relationship between APO and future stroke. RESULTS: We included 144 306 women with a total of 316 789 births in the analysis sample, of whom 17.9% had at least 1 pregnancy with an APO and 2.9% experienced an APO in ≥2 pregnancies. Women with APO had more comorbidities including obesity, hypertension, heart disease, and migraine. Median age at first stroke was 58.3 years in those with no APO, 54.8 years in those with 1 APO, and 51.6 years in those with recurrent APO. In models adjusted for sociodemographic characteristics and stroke risk factors, risk of stroke was greater in women with 1 APO (adjusted hazard ratio, 1.3 [95% CI, 1.2-1.4]) and recurrent APO (adjusted hazard ratio, 1.4 [95% CI, 1.2-1.7]) compared with those with no APO. Women with recurrent APO had more than twice the stroke risk before age 45 (adjusted odds ratio, 2.1 [95% CI, 1.5-3.1]) compared with those without APO. CONCLUSIONS: Women who experience APO have earlier onset of cerebrovascular disease, with the earliest onset in those with more than 1 affected pregnancy.

Apparent treatment-resistant hypertension associated lifetime cardiovascular risk in a longitudinal national registry.

AIMS: Apparent treatment-resistant hypertension (aRH), wherein blood pressure elevation requires treatment with multiple medications, is associated with adverse cardiovascular events over the short-term. We sought to evaluate the degree of excess risk associated with aRH across the lifespan. METHODS AND RESULTS: We identified all individuals with hypertension who were prescribed at least one anti-hypertensive medication from the FinnGen Study, a cohort of randomly selected individuals across Finland. We then identified the maximum number of concurrently prescribed anti-hypertensive medication classes prior to age 55 and classified those co-prescribed ≥4 anti-hypertensive medication classes as aRH. Using multivariable adjusted Cox proportional hazards models, we assessed the association of aRH well as the number of co-prescribed anti-hypertensive classes with cardiorenal outcomes across the lifespan. Among 48 721 hypertensive individuals, 5715 (11.7%) met the aRH criteria. Compared to those prescribed only one anti-hypertensive medication class, the lifetime risk of renal failure increased with the addition of each additional medication class, beginning with the second, while the risk of heart failure and ischaemic stroke increased after addition of the third drug class. Similarly, those with aRH suffered increased risk of renal failure (hazard ratio 2.30, 95% CI 2.00-2.65), intracranial haemorrhage (1.50, 1.08-2.05), heart failure (1.40, 1.24-1.63) cardiac death (1.79, 1.45-2.21), and all-cause death (1.76, 1.52-2.04). CONCLUSION: Among individuals with hypertension, aRH that develops prior to mid-life is associated with substantially elevated cardiorenal disease risk across the lifespan.

Examination of medical records from over 48 000 Finnish individuals found that the risk of future adverse medical events increased with a need for greater number of blood pressure medications in middle age.Using the number of blood pressure medications simultaneously prescribed before age 55, the risk of kidney problems increased with the addition of each antihypertensive medication, starting after the first, while the risk of heart failure and stroke increased with the addition of two more blood pressure medications.Individuals with very difficult to treat high blood pressure (needing at least four medications) had greater risk of nearly all assessed clinical outcomes, including death. These findings indicate that needing more medications to treat blood pressure in mid-life is associated with worse clinical outcomes. The most important goal for such patients should be to improve their blood pressure control early in life.

Associations of polygenic risk scores for preeclampsia and blood pressure with hypertensive disorders of pregnancy.

BACKGROUND: Preexisting hypertension increases risk for preeclampsia. We examined whether a generic blood pressure polygenic risk score (BP-PRS), compared with a preeclampsia-specific polygenic risk score (PE-PRS), could better predict hypertensive disorders of pregnancy. METHODS: Our study sample included 141 298 genotyped FinnGen study participants with at least one childbirth and followed from 1969 to 2021. We calculated PRSs for SBP and preeclampsia using summary statistics for greater than 1.1 million single nucleotide polymorphisms. RESULTS: We observed 8488 cases of gestational hypertension (GHT) and 6643 cases of preeclampsia. BP-PRS was associated with GHT [multivariable-adjusted hazard ratio for 1SD increase in PRS (hazard ratio 1.38; 95% CI 1.35-1.41)] and preeclampsia (1.26, 1.23-1.29), respectively. The PE-PRS was also associated with GHT (1.16; 1.14-1.19) and preeclampsia (1.21, 1.18-1.24), but with statistically more modest magnitudes of effect (P = 0.01). The model c-statistic for preeclampsia improved when PE-PRS was added to clinical risk factors (P = 4.6 × 10-15). Additional increment in the c-statistic was observed when BP-PRS was added to a model already including both clinical risk factors and PE-PRS (P = 1.1 × 10-14). CONCLUSION: BP-PRS is strongly associated with hypertensive disorders of pregnancy. Our current observations suggest that the BP-PRS could capture the genetic architecture of preeclampsia better than the current PE-PRSs. These findings also emphasize the common pathways in the development of all BP disorders. The clinical utility of a BP-PRS for preeclampsia prediction warrants further investigation.

Sex differences in coronary artery bypass grafting-related morbidity and mortality.

Background: Coronary artery bypass grafting (CABG) is associated with both cardiovascular disease (CVD) and non-CVD traits. In addition, women's prognosis after coronary events and revascularizations is worse than in men. As the course of CVD in women differs from that of men, we performed a phenome-wide analysis on the sex differences in CABG -related morbidity and mortality. Materials and methods: We performed an untargeted analysis on the sex differences in predictors and outcomes of CABG. We studied a sample of 176,680 FinnGen participants, including 5,950 individuals who underwent CABG (4,988 men and 962 women) and were followed between 1998 and 2019. Over 1,100 different traits were analyzed for both sexes and the results were adjusted with age, smoking status and BMI. Cox proportional hazards models with sex-trait interactions were used to estimate the associations between (1) traits and incident CABG; and (2) CABG and incident traits. Results: In women, CABG was more strongly related to greater increases in risk of diseases such as hypertension, Alzheimer's, aortic aneurysms, gout, and chronic kidney disease compared to risk increases observed in men (all interaction p-values < 0.03). After CABG, men had 2.5-fold (p = 3.1E-15) and women 6.3-fold (p = 9.4E-08) greater risk of cardiac death compared to same-sex individuals who did not undergo CABG (p for interaction 8.2E-4). Moreover, the risk of death in women remained higher even 12 years after CABG, whereas the long-term risk of death in men was not increased, compared to same-sex individuals who did not undergo CABG. Conclusion: The adverse outcomes after CABG, both quantity and quality, also appear to differ between men and women. In women, CABG is related to greater long-term increases in risk of cardiac death and several other disease states than in men. Consideration should therefore be given to whether women receive adequate long-term post-operative therapy and follow-up as CABG is not associated with equally improved cardiovascular disease prognosis in women than in men.

Genetic, Molecular, and Cellular Determinants of Sex-Specific Cardiovascular Traits.

Despite the well-known sex dimorphism in cardiovascular disease traits, the exact genetic, molecular, and cellular underpinnings of these differences are not well understood. A growing body of evidence currently points at the links between cardiovascular disease traits and the genome, epigenome, transcriptome, and metabolome. However, the sex-specific differences in these links remain largely unstudied due to challenges in bioinformatic methods, inadequate statistical power, analytic costs, and paucity of valid experimental models. This review article provides an overview of the literature on sex differences in genetic architecture, heritability, epigenetic changes, transcriptomic signatures, and metabolomic profiles in relation to cardiovascular disease traits. We also review the literature on the associations between sex hormones and cardiovascular disease traits and discuss the potential mechanisms underlying these associations, focusing on human studies.

Polygenic Risk Scores for Predicting Adverse Outcomes After Coronary Revascularization.

Coronary procedures predispose patients to adverse events. To improve our understanding of the genetic factors underlying postoperative prognosis, we studied the association of polygenic risk scores (PRSs) with postprocedural complications in coronary patients who underwent revascularization. The study sample comprised 8,296, 6,132, and 13,082 patients who underwent percutaneous coronary intervention, coronary artery bypass grafting, or any revascularization, respectively. We genotyped all subjects and identified adverse events during follow-up of up to 30 years by record linkage with nationwide healthcare registers. We computed PRSs for each postoperative adverse outcome (atrial fibrillation [AF], myocardial infarction, stroke, and bleeding complications) for all participants. Cox proportional hazards models were used to examine the association between PRSs and outcomes. A 1-SD increase in AF-PRS was associated with greater risk of postoperative AF with hazard ratios of 1.22 (95% confidence interval [CI] 1.16 to 1.28), 1.15 (95% CI 1.10 to 1.20) and 1.18 (95% CI 1.14 to 1.22) after percutaneous coronary intervention, coronary artery bypass grafting, and any revascularization, respectively. In contrast, the association of each PRSs with other postoperative complications was nonexistent to marginal. Inclusion of the AF-PRS in a model with a clinical risk score resulted in significant model improvement (increase in model c-statistic 0.0059 to 0.0098 depending on procedure; p <0.0002 for all). In conclusion, our results demonstrate that PRS can be used for AF risk-prediction in patients who underwent revascularization. The AF-PRS could potentially be used to improve AF prevention and outcomes in patients who underwent revascularization.

Predictors and Outcomes of Coronary Artery Bypass Grafting: A Systematic and Untargeted Analysis of More Than 120,000 Individuals and 1,300 Disease Traits.

OBJECTIVE: To perform an untargeted data-driven analysis on the correlates and outcomes of coronary artery bypass grafting (CABG). DESIGN: FinnGen cohort study. SETTING: The authors collected information on up to 1,327 disease traits before and after CABG from nationwide healthcare registers. PARTICIPANTS: A mixed population and patient sample of 127,911 individuals including 3,784 CABG patients. INTERVENTIONS: The authors assessed the association between (1) traits and incident CABG and (2) CABG and incident traits using multivariate-adjusted Cox models. MAIN RESULTS: Patients who underwent CABG and were in the fourth quartile of a risk score based on the top predictors of mortality had 12.2-fold increased risk of dying (95% confidence interval [CI], 10.3-14.5) compared with those in the first quartile. Cardiovascular disease (CVD) and CVD risk factors were most strongly associated with incident CABG. However, CABG was associated with death due to cardiac causes (hazard ratio [HR], 3.7; 95% CI, 3.5-4.0) or other causes (HR, 2.5; 95% CI, 2.4-2.7). CABG also was related to increased risk of several non-CVD traits, including anemia (HR, 3.4; 95% CI, 2.8-4.1), gastrointestinal disorders (HR, 2.2; 95% CI, 1.8-2.6), acute renal failure (HR, 4.2; 95% CI, 3.5-5.1), septicemia (HR, 3.6; 95% CI, 3.1-4.1), lung cancer (HR, 2.3; 95% CI, 1.9-2.8), Alzheimer's disease (HR, 2.5; 95% CI, 2.2-2.7), and chronic obstuctive pulmonary disease (HR, 2.5; 95% CI, 2.2-2.9). CONCLUSIONS: Known CVD risk factors associate most strongly with incident CABG. However, CABG is associated with increased risk of several, somewhat unexpected, non-CVD traits. More detailed study of these links is warranted to establish potential causality and pathogenesis.

Polygenic Risk Scores Predict Hypertension Onset and Cardiovascular Risk.

Although genetic risk scores have been used to predict hypertension, their utility in the clinical setting remains uncertain. Our study comprised N=218 792 FinnGen participants (mean age 58 years, 56% women) and N=22 624 well-phenotyped FINRISK participants (mean age 50 years, 53% women). We used public genome-wide association data to compute polygenic risk scores (PRSs) for systolic and diastolic blood pressure (BP). Using time-to-event analysis, we then assessed (1) the association of BP PRSs with hypertension and cardiovascular disease (CVD) in FinnGen and (2) the improvement in model discrimination when combining BP PRSs with the validated 4- and 10-year clinical risk scores for hypertension and CVD in FINRISK. In FinnGen, compared with having a 20 to 80 percentile range PRS, a PRS in the highest 2.5% conferred 2.3-fold (95% CI, 2.2­2.4) risk of hypertension and 10.6 years (95% CI, 9.9­11.4) earlier hypertension onset. In subgroup analyses, this risk was only 1.6-fold (95% CI, 1.5­1.7) for late-onset hypertension (age ≥55 years) but 2.8-fold (95% CI, 2.6­2.9) for early-onset hypertension (age <55 years). Elevated systolic BP PRS also conferred 1.3-fold (95% CI, 1.2­1.4) risk of CVD and 2.3 years (95% CI, 1.6­3.1) earlier onset. In FINRISK, systolic and diastolic BP PRSs improved clinical risk prediction of hypertension (but not CVD), increasing the C statistics by 0.7% (95% CI, 0.3­1.1). We demonstrate that genetic information improves hypertension risk prediction. BP PRSs together with traditional risk factors could improve prediction of hypertension and particularly early-onset hypertension, which confers substantial CVD risk.

Eukaryote specific folds: Part of the whole.

The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life. The most accepted scenarios suggest the endosymbiosis of a mitochondrial ancestor with a complex archaeon, even though the details regarding the host and the triggering factors are still being discussed. Accordingly, phylogenetic analyses have demonstrated archaeal affiliations with key informational systems, while metabolic genes are often related to bacteria, mostly to the mitochondrial ancestor. Despite of this, there exists a large number of protein families and folds found only in eukaryotes. In this study, we have analyzed structural superfamilies and folds that probably appeared during eukaryogenesis. These folds typically represent relatively small binding domains of larger multidomain proteins. They are commonly involved in biological processes that are particularly complex in eukaryotes, such as signaling, trafficking/cytoskeleton, ubiquitination, transcription and RNA processing, but according to recent studies, these processes also have prokaryotic roots. Thus the folds originating from an eukaryotic stem seem to represent accessory parts that have contributed in the expansion of several prokaryotic processes to a new level of complexity. This might have taken place as a co-evolutionary process where increasing complexity and fold innovations have supported each other.

Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core.

The folding of most integral membrane proteins follows a two-step process: initially, individual transmembrane helices are inserted into the membrane by the Sec translocon. Thereafter, these helices fold to shape the final conformation of the protein. However, for some proteins, including Aquaporin 1 (AQP1), the folding appears to follow a more complicated path. AQP1 has been reported to first insert as a four-helical intermediate, where helix 2 and 4 are not inserted into the membrane. In a second step, this intermediate is folded into a six-helical topology. During this process, the orientation of the third helix is inverted. Here, we propose a mechanism for how this reorientation could be initiated: first, helix 3 slides out from the membrane core resulting in that the preceding loop enters the membrane. The final conformation could then be formed as helix 2, 3, and 4 are inserted into the membrane and the reentrant regions come together. We find support for the first step in this process by showing that the loop preceding helix 3 can insert into the membrane. Further, hydrophobicity curves, experimentally measured insertion efficiencies and MD-simulations suggest that the barrier between these two hydrophobic regions is relatively low, supporting the idea that helix 3 can slide out of the membrane core, initiating the rearrangement process.

Why are polar residues within the membrane core evolutionary conserved?

Here, we present a study of polar residues within the membrane core of alpha-helical membrane proteins. As expected, polar residues are less frequent in the membrane than expected. Further, most of these residues are buried within the interior of the protein and are only rarely exposed to lipids. However, the polar groups often border internal water filled cavities, even if the rest of the sidechain is buried. A survey of their functional roles in known structures showed that the polar residues are often directly involved in binding of small compounds, especially in channels and transporters, but other functions including proton transfer, catalysis, and selectivity have also been attributed to these proteins. Among the polar residues histidines often interact with prosthetic groups in photosynthetic- and oxidoreductase-related proteins, whereas prolines often are required for conformational changes of the proteins. Indeed, the polar residues in the membrane core are more conserved than other residues in the core, as well as more conserved than polar residues outside the membrane. The reason is twofold; they are often (i) buried in the interior of the protein and (ii) directly involved in the function of the proteins. Finally, a method to identify which polar residues are present within the membrane core directly from protein sequences was developed. Applying the method to the set of all human membrane proteins the prediction indicates that polar residues were most frequent among active transporter proteins and GPCRs, whereas infrequent in families with few transmembrane regions, such as non-GPCR receptors.

Repositioning of transmembrane alpha-helices during membrane protein folding.

We have determined the optimal placement of individual transmembrane helices in the Pyrococcus horikoshii Glt(Ph) glutamate transporter homolog in the membrane. The results are in close agreement with theoretical predictions based on hydrophobicity, but do not, in general, match the known three-dimensional structure, suggesting that transmembrane helices can be repositioned relative to the membrane during folding and oligomerization. Theoretical analysis of a database of membrane protein structures provides additional support for this idea. These observations raise new challenges for the structure prediction of membrane proteins and suggest that the classical two-stage model often used to describe membrane protein folding needs to be modified.

Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context.

In mammalian cells, most integral membrane proteins are initially inserted into the endoplasmic reticulum membrane by the so-called Sec61 translocon. However, recent predictions suggest that many transmembrane helices (TMHs) in multispanning membrane proteins are not sufficiently hydrophobic to be recognized as such by the translocon. In this study, we have screened 16 marginally hydrophobic TMHs from membrane proteins of known three-dimensional structure. Indeed, most of these TMHs do not insert efficiently into the endoplasmic reticulum membrane by themselves. To test if loops or TMHs immediately upstream or downstream of a marginally hydrophobic helix might influence the insertion efficiency, insertion of marginally hydrophobic helices was also studied in the presence of their neighboring loops and helices. The results show that flanking loops and nearest-neighbor TMHs are sufficient to ensure the insertion of many marginally hydrophobic helices. However, for at least two of the marginally hydrophobic helices, the local interactions are not enough, indicating that post-insertional rearrangements are involved in the folding of these proteins.

Structural basis of the zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins.

Streptococcus suis Dpr is an iron-binding protein involved in oxidative stress resistance. It belongs to the bacterial Dps protein family whose members form dodecameric assemblies. Previous studies have shown that zinc and terbium inhibit iron incorporation in Listeria innocua Dps protein. In order to gain structural insights into the inhibitory effect of zinc and terbium, the crystal structures of Streptococcus suis Dpr complexes with these ions were determined at 1.8 A and 2.1 A, respectively. Both ions were found to bind at the ferroxidase center and in the same location as iron. In addition, a novel zinc-binding site formed by His40 and His44 was identified. Both His residues were found to be present within all known Streptococcus suis Dpr variants and in Streptococcus pneumoniae, Streptococcus gordonii, and Streptococcus sanguinis Dpr proteins. Amino acid sequence alignment of Dpr with other Dps family members revealed that His44 is highly conserved, in contrast to His40. The inhibitory effect of zinc and terbium on iron oxidation in Dpr was studied in vitro, and it was found that both ions at concentrations >0.2 mM almost completely abolish iron binding. These results provide a structural basis for the inhibitory effect of zinc and terbium in the Dps family of proteins, and suggest a potential role of the Dps proteins in zinc detoxification mechanisms involving the second zinc-binding site.

Coils in the membrane core are conserved and functionally important.

With the increasing number of available alpha-helical transmembrane (TM) protein structures, the traditional picture of membrane proteins has been challenged. For example, reentrant regions, which enter and exit the membrane at the same side, and interface helices, which lie parallel with the membrane in the membrane-water interface, are common. Furthermore, TM helices are frequently kinked, and their length and tilt angle vary. Here, we systematically analyze 7% of all residues within the deep membrane core that are in coil state. These coils can be found in TM-helix kinks as major breaks in TM helices and as parts of reentrant regions. Coil residues are significantly more conserved than other residues. Due to the polar character of the coil backbone, they are either buried or located near aqueous channels. Coil residues are frequently found within channels and transporters, where they introduce the flexibility and polarity required for transport across the membrane. Therefore, we believe that coil residues in the membrane core, while constituting a structural anomaly, are essential for the function of proteins.